Arsenic meta-analysis, DMPs and DVPs, common CpGs

Required Packages

library(missMethyl)
library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
library(kableExtra)
library(IlluminaHumanMethylation450kanno.ilmn12.hg19)
library(dplyr)

ann850k = getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
ann450k = getAnnotation(IlluminaHumanMethylation450kanno.ilmn12.hg19)

ann450kUnique = ann450k[!(rownames(ann450k) %in% rownames(ann850k)),]
dim(ann450kUnique)
# 33059    33

annAll = rbind(ann850k[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")], ann450kUnique[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")])
annAll = data.frame(annAll)

setwd('/Users/annebozack/Documents/arsenic_meta/generic-metal')

Functions

metalProcess = function(table, anno){
    colnames(table) = table[1,]
    colnames(table)[1] = 'Name'
    table = table[-1,]
    table = table[,-c(2,3)]
    table[,2] = as.numeric(table[,2])
    table[,3] = as.numeric(table[,3])
    table[,4] = as.numeric(table[,4])

    table$P.FDR = p.adjust(table[,4], method='fdr')
    table$P.Bonf = p.adjust(table[,4], method='bonferroni')
    
    table = merge(table, annAll, by = 'Name', all.y = F)
    table = data.frame(table)
    
    table = table[order(table[,4]),]

    return(table)
}

manhattan_meta = function(probe, colors = c("#2D728F", "#2B4162"), FDR = FALSE){
    probe$chr = as.numeric(gsub("chr", "", probe$chr))

    don = probe %>% 
        # Compute chromosome size
            group_by(chr) %>% summarise(chr_len=as.numeric(max(pos))) %>% 
        # Calculate cumulative position of each chromosome
            mutate(tot=cumsum(chr_len)-chr_len) %>% dplyr::select(-chr_len) %>%
        # Add this info to the initial dataset
            left_join(probe, ., by=c("chr"="chr")) %>%
        # Add a cumulative position of each site
            arrange(chr, pos) %>% mutate(poscum=pos+tot) # %>%
        # Add highlight and annotation information
            # mutate(is_highlight=ifelse(SNP %in% snpsOfInterest, "yes", "no")) %>%
            # mutate(is_annotate_fdr=ifelse(adj.P.Val<0.05 & adj.P.Val.bonf>0.05, "yes", "no")) %>%
            # mutate(is_annotate_bonf=ifelse(adj.P.Val.bonf <0.05, "yes", "no"))
            # don$alpha[don$is_annotate_fdr == 'no'] = 0.6
            # don$alpha[don$is_annotate_fdr == 'yes'] = 0
        # Prepare X axis
            axisdf = don %>% group_by(chr) %>% summarize(center=(max(poscum) + min(poscum))/2)
    don = merge(don, probe[,c(1,11)], on='cpg', all.x=T)
    
    if (FDR){
        FRDalpha = 0.5
    } else {
        FRDalpha = 0
    }

    manhattan = ggplot(don, aes(x=poscum, y=-log10(P.value))) +
    geom_point(aes(color=as.factor(chr)), size=0.8, alpha = 0.55) + scale_color_manual(values = rep(colors, dim(table(don$chr)))) +
    # p-value cutoffs
    geom_hline(yintercept=-log10(0.05/nrow(don)), colour = '#AB3428', size=.3, alpha = 0.5) +
    geom_hline(yintercept=-log10(max(don$P.value[don$P.FDR < 0.05])), colour='#AB3428', size=.3, alpha = FRDalpha, linetype = "dashed") +
    # custom axes:
    scale_x_continuous(expand = c(0.005, 0.005), limits = c(min(don$poscum), max(don$poscum)), label = axisdf$chr, breaks= axisdf$center) +
    scale_y_continuous(expand = c(0, 0), limits = c(0, (max(-log10(don$P.value)) + 0.5)), breaks = seq(from = 0, to = (max(-log10(don$P.value)) + 0.5), by = 1)) + 
    # Custom theme:
    theme_minimal() + theme( 
    legend.position="none", panel.border = element_blank(), panel.grid.minor.y = element_blank(), panel.grid.major.x = element_blank(), panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line(size = 0.2, color = 'gray65')) + theme(text = element_text(size = 7.5)) + 
    labs(y=expression(-log[10]*"(P-value)"), x='Chromosome') 
    
    return(manhattan)
}

lambda <- function(p) median(qchisq(p, df=1, lower.tail=FALSE), na.rm=TRUE) / qchisq(0.5, df=1)

gg_qqplot = function(pvector) {
    l = round(lambda(pvector), 3)
    o = -log10(sort(pvector, decreasing = FALSE))
    e = -log10(ppoints(length(pvector)))
    df = data.frame(o = o, e = e)
    ggplot(df, aes(e, o)) + geom_point(alpha = 0.5, size = 1) + geom_abline(intercept = 0, slope = 1, color = '#AB3428') + labs(y = expression(Observed ~ ~-log[10](italic(p))), x = expression(Expected ~ ~-log[10](italic(p)))) + theme_classic() + annotate("text", x = 1, y = 5, label = paste0('λ = ', l))
}


volcano_meta = function(probe, FDR = FALSE) {
        if (FDR){
            FDRalpha = 0.5
        } else {
            FDRalpha = 0
        }
        
        volcano = ggplot(probe, aes(x= Effect, y = -log10(P.value))) + 
        geom_point(size = 0.8, alpha=0.4) + 
        geom_hline(aes(yintercept = -log10(0.05/nrow(probe)), color = "#AB3428", alpha = 0.5)) + 
        geom_hline(aes(yintercept = -log10(max(P.value[P.FDR < 0.05]))), color = "#AB3428", alpha = FDRalpha, linetype = "dashed") + theme_minimal() + 
        labs(y=expression(-log[10]*"(P-value)"), x='Effect estimate') + theme(panel.grid.minor.y = element_blank()) + theme(text = element_text(size=8)) + 
        scale_y_continuous(expand = c(0, 0), limits = c(0, (max(-log10(probe$P.value)) + 0.5)), breaks = seq(from = 0, to = (max(-log10(probe$P.value)) + 0.5), by = 1)) +
        theme(legend.position="none") + theme(panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line(size = 0.2, color = 'gray65'), panel.grid.major.x = element_line(size = 0.2, color = 'gray65'))
        
        return(volcano)
}

DMPs

DMP datasets for common CpGs

# results adjusted for age, sex, smoking

fact850 = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450 = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMC = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DMPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)
chileBuccal = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DMPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)

allCpg = Reduce(intersect, list(fact850$cpg, fact450$cpg, chilePBMC$cpg, chileBuccal$cpg))

fact850 = fact850[fact850$cpg %in% allCpg,]
fact450 = fact450[fact450$cpg %in% allCpg,]
chilePBMC = chilePBMC[chilePBMC$cpg %in% allCpg,]
chileBuccal = chileBuccal[chileBuccal$cpg %in% allCpg,]

write.table(fact850, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMC, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccal, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)


# results adjusted for age, sex, smoking, cells

fact850cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMCcell = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DMPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)
chileBuccalcell = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DMPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)

fact850cell = fact850cell[fact850cell$cpg %in% allCpg,]
fact450cell = fact450cell[fact450cell$cpg %in% allCpg,]
chilePBMCcell = chilePBMCcell[chilePBMCcell $cpg %in% allCpg,]
chileBuccalcell = chileBuccalcell[chileBuccalcell$cpg %in% allCpg,]

write.table(fact850cell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450cell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMCcell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccalcell, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)

Run in METAL

cd /Users/annebozack/Documents/arsenic_meta/generic-metal

MARKER "cpg"
EFFECT "logFC"
PVAL "P.exitValue"
STDERR "std_err"
SCHEME STDERR

# SCHEME STDERR command and weights effect size estimates using the inverse of the corresponding standard errors
    
# no cell type adjustment, blood only
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_032921 .tbl

ANALYZE HETEROGENEITY

# no cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_120420 .tbl

ANALYZE

# cell type adjustment, blood only  
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_120420 .tbl

ANALYZE

# cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DMP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_120420 .tbl

ANALYZE

Without cell type adjustment

Blood only

metal_blood_noCell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_1204201.tbl', sep = "\t")

metal_blood_noCell = metalProcess(metal_blood_noCell)

write.csv(metal_blood_noCell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_blood_no_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_blood_noCell$P.value < 0.05)
#  FALSE   TRUE 
# 357719  19632 

# FDR
table(metal_blood_noCell$P.FDR < 0.05)
# FALSE 
# 377351 

table(metal_blood_noCell$P.FDR < 0.1)
# FALSE 
# 377351 

# Bonferroni
table(metal_blood_noCell$P.Bonf < 0.05)
# FALSE 
# 377351 


# GO analysis, FDR < 0.1 probes

# NA


# Plotting

gg_qqplot(metal_blood_noCell$P.value)
quartz.save('qq_metal_blood_noCell_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_blood_noCell)
quartz.save('manhattan_metal_blood_noCell_120420.png', type = "png", dpi = 300)

volcano_meta(metal_blood_noCell)
quartz.save('volcano_metal_blood_noCell_120420.png', type = "png", dpi = 300)

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_noCell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_noCell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_noCell_120420.png")

Top 100 probes

X	Name	Effect	StdErr	P.value	Direction	P.FDR	P.Bonf	chr	pos	UCSC_RefGene_Name	UCSC_RefGene_Group
93	cg00004257	0.2473	0.0503	0.0000009	+++	0.1315697	0.3325217	chr1	34629175	CSMD2	Body
316516	cg22938488	0.1765	0.0365	0.0000013	-++	0.1315697	0.5045183	chr5	1501670	LPCAT1	Body
114376	cg07490485	0.1711	0.0356	0.0000016	+++	0.1315697	0.5924411	chr14	50432614
194923	cg13490635	0.2572	0.0537	0.0000016	+++	0.1315697	0.6207424	chr8	30242021	RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS	5’UTR;5’UTR;1stExon;1stExon;1stExon;5’UTR;1stExon;5’UTR
17421	cg01050273	-0.2598	0.0545	0.0000019	–+	0.1315697	0.7064011	chr14	101120705
129233	cg08528486	0.1663	0.0350	0.0000021	-+-	0.1315697	0.7894183	chr13	113648767	MCF2L;MCF2L	Body;Body
248565	cg17342864	0.1239	0.0268	0.0000036	++-	0.1950905	1.0000000	chr2	239973967	HDAC4	3’UTR
39707	cg02483029	0.3626	0.0795	0.0000051	++-	0.2263687	1.0000000	chr8	48297271	KIAA0146	Body
359036	cg26299756	0.2130	0.0468	0.0000054	+++	0.2263687	1.0000000	chr6	85478807
73319	cg04685632	-0.1960	0.0437	0.0000073	—	0.2749002	1.0000000	chr20	62082611	KCNQ2;KCNQ2;KCNQ2;KCNQ2;KCNQ2	Body;Body;Body;Body;Body
182880	cg12547807	-0.2121	0.0478	0.0000090	—	0.2996167	1.0000000	chr1	9473751
46132	cg02892755	-0.2760	0.0627	0.0000106	—	0.2996167	1.0000000	chr1	28103358	STX12	Body
233149	cg16190478	0.2482	0.0566	0.0000118	+++	0.2996167	1.0000000	chr21	45789122	TRPM2	Body
20130	cg01218206	-0.2722	0.0621	0.0000118	—	0.2996167	1.0000000	chr11	116933977	SIK3	Body
138847	cg09233730	0.1233	0.0281	0.0000119	++-	0.2996167	1.0000000	chr1	1688446	NADK	Body
290023	cg20692268	-0.2330	0.0538	0.0000146	—	0.3155846	1.0000000	chr1	25358981
295061	cg21122375	-0.2208	0.0510	0.0000151	+–	0.3155846	1.0000000	chr7	37956869	SFRP4	TSS1500
3844	cg00226545	0.4875	0.1129	0.0000158	+++	0.3155846	1.0000000	chr16	54320225	IRX3;IRX3	5’UTR;1stExon
297084	cg21264207	0.2006	0.0465	0.0000159	+++	0.3155846	1.0000000	chr10	64576130	EGR2;EGR2;EGR2;EGR2	TSS200;5’UTR;TSS200;TSS200
225228	cg15572907	0.4507	0.1050	0.0000175	+++	0.3173342	1.0000000	chr19	40995921	SPTBN4	Body
220977	cg15206981	-0.1814	0.0423	0.0000177	—	0.3173342	1.0000000	chr4	124323013	SPRY1;SPRY1	Body;Body
252559	cg17679619	-0.2640	0.0617	0.0000190	—	0.3250364	1.0000000	chr4	74542972
110843	cg07242931	0.1968	0.0466	0.0000242	++-	0.3975311	1.0000000	chr1	26034297	MAN1C1	Body
316408	cg22930549	-0.2602	0.0623	0.0000297	—	0.4198030	1.0000000	chr14	68779833	RAD51L1;RAD51L1;RAD51L1	Body;Body;Body
330525	cg24029819	0.1850	0.0443	0.0000299	+++	0.4198030	1.0000000	chr7	157550679	PTPRN2;PTPRN2;PTPRN2	Body;Body;Body
223120	cg15396310	-0.1523	0.0366	0.0000311	—	0.4198030	1.0000000	chr7	72971398	BCL7B	Body
222024	cg15300814	0.1316	0.0316	0.0000312	-++	0.4198030	1.0000000	chr6	111580238	KIAA1919	TSS1500
244019	cg16994941	-0.1645	0.0395	0.0000315	–+	0.4198030	1.0000000	chr5	141218887
173665	cg11832210	0.4302	0.1036	0.0000331	+++	0.4198030	1.0000000	chr10	91295346	SLC16A12	TSS200
80050	cg05137378	0.1421	0.0343	0.0000338	+++	0.4198030	1.0000000	chr1	58393137	DAB1	5’UTR
187142	cg12890388	0.1242	0.0300	0.0000347	-++	0.4198030	1.0000000	chr20	10412709	MKKS;MKKS	5’UTR;TSS200
249040	cg17382048	-0.2526	0.0611	0.0000356	—	0.4198030	1.0000000	chr11	118754386	CXCR5	TSS200
263306	cg18513383	0.1561	0.0380	0.0000397	+++	0.4277078	1.0000000	chr4	57181518	KIAA1211	Body
110963	cg07252171	0.1291	0.0314	0.0000400	+++	0.4277078	1.0000000	chr5	573376
182554	cg12518360	-0.1890	0.0461	0.0000408	—	0.4277078	1.0000000	chr11	92931304	SLC36A4	TSS1500
242633	cg16876219	-0.1940	0.0475	0.0000442	—	0.4277078	1.0000000	chr3	197222311
139515	cg09275980	0.2946	0.0722	0.0000446	+++	0.4277078	1.0000000	chr15	25350925	SNORD116-29	TSS1500
168526	cg11434671	-0.1587	0.0389	0.0000453	—	0.4277078	1.0000000	chr17	74524611	CYGB	3’UTR
126827	cg08354093	0.2571	0.0631	0.0000456	++-	0.4277078	1.0000000	chr20	23029640	THBD	1stExon
70534	cg04498082	-0.1478	0.0363	0.0000474	—	0.4277078	1.0000000	chr11	356222
74243	cg04752680	-0.1173	0.0289	0.0000482	—	0.4277078	1.0000000	chr19	14114100	RFX1	5’UTR
69163	cg04402095	-0.1163	0.0286	0.0000484	—	0.4277078	1.0000000	chr1	156721844	HDGF;HDGF;HDGF	Body;1stExon;TSS1500
196521	cg13586599	0.1198	0.0295	0.0000494	+++	0.4277078	1.0000000	chr6	25652383	SCGN	TSS200
370510	cg27144039	-0.1489	0.0369	0.0000539	—	0.4277078	1.0000000	chr20	62605308
304157	cg21880328	0.0981	0.0243	0.0000546	+++	0.4277078	1.0000000	chr7	117514017	CTTNBP2	TSS1500
187085	cg12884605	0.1307	0.0324	0.0000550	-++	0.4277078	1.0000000	chr12	66123314
27848	cg01729837	0.1537	0.0381	0.0000557	+++	0.4277078	1.0000000	chr19	719622	PALM;PALM	Body;Body
353515	cg25869889	0.1542	0.0383	0.0000576	-++	0.4277078	1.0000000	chr11	6436464	APBB1;APBB1	5’UTR;5’UTR
245138	cg17083982	0.1892	0.0472	0.0000604	+++	0.4277078	1.0000000	chr12	57946083	KIF5A	Body
372554	cg27305735	0.5261	0.1312	0.0000609	-++	0.4277078	1.0000000	chr1	247537369
351351	cg25687423	-0.1458	0.0364	0.0000618	—	0.4277078	1.0000000	chr6	43193521	C6orf108;C6orf108	Body;3’UTR
308288	cg22244986	-0.2426	0.0606	0.0000620	—	0.4277078	1.0000000	chr1	201405370
376680	cg27618777	-0.2320	0.0580	0.0000631	—	0.4277078	1.0000000	chr6	32804628	TAP2;TAP2	Body;Body
222274	cg15323873	-0.1528	0.0382	0.0000631	+–	0.4277078	1.0000000	chr10	79650526	DLG5	Body
315429	cg22853526	0.1573	0.0393	0.0000635	++-	0.4277078	1.0000000	chr1	113216965	MOV10;MOV10	TSS200;TSS200
11514	cg00688297	-0.3468	0.0868	0.0000641	—	0.4277078	1.0000000	chr8	145752292	LRRC24;MGC70857	5’UTR;3’UTR
374551	cg27455890	0.3364	0.0843	0.0000655	-+-	0.4277078	1.0000000	chr10	118976677
189609	cg13100118	-0.2271	0.0569	0.0000657	—	0.4277078	1.0000000	chr1	19795369	CAPZB	Body
17436	cg01051581	-0.1554	0.0390	0.0000669	—	0.4280695	1.0000000	chr5	32090639	PDZD2	Body
191378	cg13253153	0.1418	0.0356	0.0000683	++-	0.4293625	1.0000000	chr11	2826988	KCNQ1;KCNQ1	Body;Body
306721	cg22111078	0.4197	0.1058	0.0000729	+++	0.4468179	1.0000000	chr5	172655925
350973	cg25652701	0.2459	0.0621	0.0000747	-++	0.4468179	1.0000000	chr7	105348517	ATXN7L1	Body
278372	cg19739774	-0.2022	0.0511	0.0000766	—	0.4468179	1.0000000	chr7	7711168	RPA3	5’UTR
270820	cg19131667	-0.1760	0.0445	0.0000779	—	0.4468179	1.0000000	chr3	17236940	TBC1D5;TBC1D5;TBC1D5	Body;Body;Body
140584	cg09353063	0.1687	0.0427	0.0000779	+++	0.4468179	1.0000000	chr3	8811092	OXTR;OXTR	1stExon;5’UTR
325184	cg23618638	0.2799	0.0709	0.0000782	++-	0.4468179	1.0000000	chr7	22123315
324549	cg23558842	0.3019	0.0766	0.0000816	+++	0.4532511	1.0000000	chr11	15095178	CALCB;CALCB	1stExon;5’UTR
30461	cg01895740	0.1191	0.0303	0.0000834	-++	0.4532511	1.0000000	chr19	7852739	CLEC4GP1	Body
115584	cg07572317	0.1241	0.0316	0.0000842	-++	0.4532511	1.0000000	chr10	135029782	KNDC1	Body
207752	cg14276580	-0.1726	0.0439	0.0000855	—	0.4532511	1.0000000	chr13	40527020
28749	cg01787808	-0.2151	0.0548	0.0000871	—	0.4532511	1.0000000	chr15	34502580	C15orf29	TSS1500
142227	cg09470219	0.1538	0.0392	0.0000880	-++	0.4532511	1.0000000	chr16	22378015	CDR2	Body
150380	cg10079131	0.1186	0.0303	0.0000897	+++	0.4532511	1.0000000	chr11	688397	DEAF1	Body
96562	cg06302806	0.1502	0.0383	0.0000898	-++	0.4532511	1.0000000	chr20	43939970	RBPJL	Body
284248	cg20201957	0.1346	0.0344	0.0000914	+++	0.4532511	1.0000000	chr17	2603638	KIAA0664	Body
91725	cg05945266	0.1368	0.0350	0.0000919	++-	0.4532511	1.0000000	chr17	80545020	FOXK2	Body
65453	cg04159878	0.2325	0.0595	0.0000933	-++	0.4532511	1.0000000	chr1	110179127
4536	cg00268744	0.1620	0.0415	0.0000944	++-	0.4532511	1.0000000	chr16	68281186	PLA2G15	Body
228569	cg15827214	0.1445	0.0370	0.0000949	-++	0.4532511	1.0000000	chr8	80522324	STMN2	TSS1500
366745	cg26870057	-0.2425	0.0622	0.0000967	—	0.4553062	1.0000000	chr2	118947242
301518	cg21648245	-0.2749	0.0706	0.0000988	–+	0.4553062	1.0000000	chr4	109541405	LOC285456;RPL34;RPL34	Body;TSS1500;TSS1500
97877	cg06399735	0.1720	0.0442	0.0000989	+++	0.4553062	1.0000000	chr8	18836280	PSD3	Body
276528	cg19599951	-0.2648	0.0682	0.0001020	—	0.4571093	1.0000000	chr11	118754280	CXCR5	TSS1500
250289	cg17478979	0.1844	0.0475	0.0001022	-++	0.4571093	1.0000000	chr6	149772150	ZC3H12D	Body
186512	cg12835806	-0.1459	0.0376	0.0001045	—	0.4571093	1.0000000	chr16	2812435	SRRM2	Body
261431	cg18370318	0.1477	0.0381	0.0001063	+++	0.4571093	1.0000000	chr1	16258580	SPEN	Body
17195	cg01036779	-0.1355	0.0350	0.0001064	—	0.4571093	1.0000000	chr19	6768251	SH2D3A	TSS1500
370466	cg27141509	-0.2598	0.0670	0.0001066	–+	0.4571093	1.0000000	chr10	5886111
254669	cg17854066	0.1884	0.0489	0.0001164	+++	0.4806260	1.0000000	chr4	55575932	KIT;KIT	Body;Body
128249	cg08460812	-0.2211	0.0574	0.0001168	–+	0.4806260	1.0000000	chr4	109087419	LOC641518;LEF1;LEF1;LEF1;LEF1	TSS1500;Body;Body;Body;Body
227288	cg15720669	0.3590	0.0933	0.0001183	+++	0.4806260	1.0000000	chr3	138666040	FOXL2;C3orf72	TSS200;TSS200
108350	cg07090074	0.1832	0.0476	0.0001185	+++	0.4806260	1.0000000	chr16	69457218	CYB5B	TSS1500
17258	cg01041239	0.1897	0.0493	0.0001209	++-	0.4806260	1.0000000	chr18	13222581	C18orf1;C18orf1	5’UTR;5’UTR
198286	cg13692433	0.1526	0.0397	0.0001209	+++	0.4806260	1.0000000	chr11	112832159	NCAM1;NCAM1;NCAM1;NCAM1;NCAM1;NCAM1	1stExon;5’UTR;5’UTR;1stExon;5’UTR;1stExon
298451	cg21405786	0.1850	0.0481	0.0001210	+++	0.4806260	1.0000000	chr7	148990485	ZNF783	Body
141105	cg09390241	-0.1942	0.0506	0.0001225	—	0.4815156	1.0000000	chr4	8174148
199983	cg13802583	0.2841	0.0741	0.0001253	+++	0.4874441	1.0000000	chr12	130961453	RIMBP2	Body
370211	cg27123273	-0.1284	0.0335	0.0001275	—	0.4909414	1.0000000	chr16	72405329
76726	cg04911180	-0.2970	0.0776	0.0001295	–+	0.4916344	1.0000000	chr3	176775716	TBL1XR1	Body
323848	cg23504707	0.1422	0.0372	0.0001304	+++	0.4916344	1.0000000	chr14	60712563	PPM1A;PPM1A	5’UTR;1stExon

---

Including buccal

metal_all_noCell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_1204201.tbl', sep = "\t")

metal_all_noCell = metalProcess(metal_all_noCell)

write.csv(metal_all_noCell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_all_no_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_all_noCell$P.value < 0.05)
#  FALSE   TRUE 
# 356030  21321 

# FDR
table(metal_all_noCell$P.FDR < 0.05)
# FALSE 
# 377351 

table(metal_all_noCell$P.FDR < 0.1)
#  FALSE   TRUE 
#  377348    3 

# Bonferroni
table(metal_all_noCell$P.Bonf < 0.05)
# FALSE 
# 377351  


# GO analysis, FDR < 0.1 probes

annAll2 = rbind(ann850k[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")], ann450kUnique[,c('Name', 'chr', 'pos', "UCSC_RefGene_Name", "UCSC_RefGene_Group")])

go_metal_all_noCell = gometh(sig.cpg = metal_all_noCell$Name[metal_all_noCell$P.FDR < 0.1], all.cpg = metal_all_noCell$Name, array.type = '450K', anno = annAll2)
go_metal_all_noCell = go_metal_all_noCell[order(go_metal_all_noCell$P.DE),]

table(go_metal_all_noCell$P.DE<0.05)
# FALSE  TRUE 
# 22516    46

table(go_metal_all_noCell$FDR<0.05)
# FALSE 
# 22557 

write.csv(go_metal_all_noCell[go_metal_all_noCell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DMP_all_no_cell_common_120420.csv')


# KEGG analysis, FDR < 0.1 probes

kegg_metal_all_noCell = gometh(sig.cpg = metal_all_noCell$Name[metal_all_noCell$P.FDR < 0.1], all.cpg = metal_all_noCell$Name, collection = 'KEGG', array.type = '450K', anno = annAll2)
kegg_metal_all_noCell = kegg_metal_all_noCell[order(kegg_metal_all_noCell$P.DE),]

table(kegg_metal_all_noCell$P.DE<0.05)
# FALSE  TRUE 
# 338     2 

table(kegg_metal_all_noCell$FDR<0.05)
# FALSE 
# 340

write.csv(kegg_metal_all_noCell[kegg_metal_all_noCell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DMP_all_no_cell_common_120420.csv')


# Plotting

gg_qqplot(metal_all_noCell$P.value)
quartz.save('qq_metal_all_noCell_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_all_noCell)
quartz.save('manhattan_metal_all_noCell_120420.png', type = "png", dpi = 300)

volcano_meta(metal_all_noCell)
quartz.save('volcano_metal_all_noCell_120420.png', type = "png", dpi = 300)

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_noCell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_noCell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_noCell_120420.png")

Top 100 probes

	X	Description	N	DE	P.DE	FDR
1	path:hsa00565	Ether lipid metabolism	49	1	0.0039233	1
2	path:hsa00564	Glycerophospholipid metabolism	92	1	0.0156145	1
NA	NA	NA	NA	NA	NA	NA
NA.1	NA	NA	NA	NA	NA	NA
NA.2	NA	NA	NA	NA	NA	NA
NA.3	NA	NA	NA	NA	NA	NA
NA.4	NA	NA	NA	NA	NA	NA
NA.5	NA	NA	NA	NA	NA	NA
NA.6	NA	NA	NA	NA	NA	NA
NA.7	NA	NA	NA	NA	NA	NA
NA.8	NA	NA	NA	NA	NA	NA
NA.9	NA	NA	NA	NA	NA	NA
NA.10	NA	NA	NA	NA	NA	NA
NA.11	NA	NA	NA	NA	NA	NA
NA.12	NA	NA	NA	NA	NA	NA
NA.13	NA	NA	NA	NA	NA	NA
NA.14	NA	NA	NA	NA	NA	NA
NA.15	NA	NA	NA	NA	NA	NA
NA.16	NA	NA	NA	NA	NA	NA
NA.17	NA	NA	NA	NA	NA	NA
NA.18	NA	NA	NA	NA	NA	NA
NA.19	NA	NA	NA	NA	NA	NA
NA.20	NA	NA	NA	NA	NA	NA
NA.21	NA	NA	NA	NA	NA	NA
NA.22	NA	NA	NA	NA	NA	NA
NA.23	NA	NA	NA	NA	NA	NA
NA.24	NA	NA	NA	NA	NA	NA
NA.25	NA	NA	NA	NA	NA	NA
NA.26	NA	NA	NA	NA	NA	NA
NA.27	NA	NA	NA	NA	NA	NA
NA.28	NA	NA	NA	NA	NA	NA
NA.29	NA	NA	NA	NA	NA	NA
NA.30	NA	NA	NA	NA	NA	NA
NA.31	NA	NA	NA	NA	NA	NA
NA.32	NA	NA	NA	NA	NA	NA
NA.33	NA	NA	NA	NA	NA	NA
NA.34	NA	NA	NA	NA	NA	NA
NA.35	NA	NA	NA	NA	NA	NA
NA.36	NA	NA	NA	NA	NA	NA
NA.37	NA	NA	NA	NA	NA	NA
NA.38	NA	NA	NA	NA	NA	NA
NA.39	NA	NA	NA	NA	NA	NA
NA.40	NA	NA	NA	NA	NA	NA
NA.41	NA	NA	NA	NA	NA	NA
NA.42	NA	NA	NA	NA	NA	NA
NA.43	NA	NA	NA	NA	NA	NA
NA.44	NA	NA	NA	NA	NA	NA
NA.45	NA	NA	NA	NA	NA	NA
NA.46	NA	NA	NA	NA	NA	NA
NA.47	NA	NA	NA	NA	NA	NA
NA.48	NA	NA	NA	NA	NA	NA
NA.49	NA	NA	NA	NA	NA	NA
NA.50	NA	NA	NA	NA	NA	NA
NA.51	NA	NA	NA	NA	NA	NA
NA.52	NA	NA	NA	NA	NA	NA
NA.53	NA	NA	NA	NA	NA	NA
NA.54	NA	NA	NA	NA	NA	NA
NA.55	NA	NA	NA	NA	NA	NA
NA.56	NA	NA	NA	NA	NA	NA
NA.57	NA	NA	NA	NA	NA	NA
NA.58	NA	NA	NA	NA	NA	NA
NA.59	NA	NA	NA	NA	NA	NA
NA.60	NA	NA	NA	NA	NA	NA
NA.61	NA	NA	NA	NA	NA	NA
NA.62	NA	NA	NA	NA	NA	NA
NA.63	NA	NA	NA	NA	NA	NA
NA.64	NA	NA	NA	NA	NA	NA
NA.65	NA	NA	NA	NA	NA	NA
NA.66	NA	NA	NA	NA	NA	NA
NA.67	NA	NA	NA	NA	NA	NA
NA.68	NA	NA	NA	NA	NA	NA
NA.69	NA	NA	NA	NA	NA	NA
NA.70	NA	NA	NA	NA	NA	NA
NA.71	NA	NA	NA	NA	NA	NA
NA.72	NA	NA	NA	NA	NA	NA
NA.73	NA	NA	NA	NA	NA	NA
NA.74	NA	NA	NA	NA	NA	NA
NA.75	NA	NA	NA	NA	NA	NA
NA.76	NA	NA	NA	NA	NA	NA
NA.77	NA	NA	NA	NA	NA	NA
NA.78	NA	NA	NA	NA	NA	NA
NA.79	NA	NA	NA	NA	NA	NA
NA.80	NA	NA	NA	NA	NA	NA
NA.81	NA	NA	NA	NA	NA	NA
NA.82	NA	NA	NA	NA	NA	NA
NA.83	NA	NA	NA	NA	NA	NA
NA.84	NA	NA	NA	NA	NA	NA
NA.85	NA	NA	NA	NA	NA	NA
NA.86	NA	NA	NA	NA	NA	NA
NA.87	NA	NA	NA	NA	NA	NA
NA.88	NA	NA	NA	NA	NA	NA
NA.89	NA	NA	NA	NA	NA	NA
NA.90	NA	NA	NA	NA	NA	NA
NA.91	NA	NA	NA	NA	NA	NA
NA.92	NA	NA	NA	NA	NA	NA
NA.93	NA	NA	NA	NA	NA	NA
NA.94	NA	NA	NA	NA	NA	NA
NA.95	NA	NA	NA	NA	NA	NA
NA.96	NA	NA	NA	NA	NA	NA
NA.97	NA	NA	NA	NA	NA	NA

---

Top 100 GO terms

	X	ONTOLOGY	TERM	N	DE	P.DE	FDR
1	GO:0047191	MF	1-alkylglycerophosphocholine O-acyltransferase activity	1	1	0.0009633	1
2	GO:2001246	BP	negative regulation of phosphatidylcholine biosynthetic process	1	1	0.0009633	1
3	GO:0047159	MF	1-alkenylglycerophosphocholine O-acyltransferase activity	2	1	0.0009633	1
4	GO:0050200	MF	plasmalogen synthase activity	2	1	0.0009633	1
5	GO:0047192	MF	1-alkylglycerophosphocholine O-acetyltransferase activity	3	1	0.0010256	1
6	GO:0047184	MF	1-acylglycerophosphocholine O-acyltransferase activity	4	1	0.0010256	1
7	GO:0016413	MF	O-acetyltransferase activity	7	1	0.0014116	1
8	GO:2001245	BP	regulation of phosphatidylcholine biosynthetic process	5	1	0.0016745	1
9	GO:0036148	BP	phosphatidylglycerol acyl-chain remodeling	18	1	0.0018954	1
10	GO:0043129	BP	surfactant homeostasis	9	1	0.0020195	1
11	GO:0048875	BP	chemical homeostasis within a tissue	11	1	0.0020229	1
12	GO:0036151	BP	phosphatidylcholine acyl-chain remodeling	29	1	0.0027444	1
13	GO:0150172	BP	regulation of phosphatidylcholine metabolic process	8	1	0.0029006	1
14	GO:0003841	MF	1-acylglycerol-3-phosphate O-acyltransferase activity	13	1	0.0038687	1
15	GO:0016411	MF	acylglycerol O-acyltransferase activity	19	1	0.0038688	1
16	GO:0046471	BP	phosphatidylglycerol metabolic process	33	1	0.0040670	1
17	GO:0071072	BP	negative regulation of phospholipid biosynthetic process	7	1	0.0042526	1
18	GO:0042171	MF	lysophosphatidic acid acyltransferase activity	15	1	0.0043004	1
19	GO:0071617	MF	lysophospholipid acyltransferase activity	17	1	0.0043626	1
20	GO:0035577	CC	azurophil granule membrane	54	1	0.0048208	1
21	GO:0008374	MF	O-acyltransferase activity	42	1	0.0058474	1
22	GO:0071071	BP	regulation of phospholipid biosynthetic process	19	1	0.0063761	1
23	GO:1903726	BP	negative regulation of phospholipid metabolic process	13	1	0.0063958	1
24	GO:0006656	BP	phosphatidylcholine biosynthetic process	38	1	0.0076155	1
25	GO:0016407	MF	acetyltransferase activity	92	1	0.0080324	1
26	GO:0006654	BP	phosphatidic acid biosynthetic process	47	1	0.0099298	1
27	GO:0051055	BP	negative regulation of lipid biosynthetic process	54	1	0.0099924	1
28	GO:0046473	BP	phosphatidic acid metabolic process	49	1	0.0104286	1
29	GO:0005811	CC	lipid droplet	85	1	0.0106104	1
30	GO:0046470	BP	phosphatidylcholine metabolic process	86	1	0.0123996	1
31	GO:0005766	CC	primary lysosome	142	1	0.0138020	1
32	GO:0042582	CC	azurophil granule	142	1	0.0138020	1
33	GO:0045833	BP	negative regulation of lipid metabolic process	93	1	0.0165409	1
34	GO:0016747	MF	transferase activity, transferring acyl groups other than amino-acyl groups	200	1	0.0197092	1
35	GO:0016746	MF	transferase activity, transferring acyl groups	228	1	0.0214958	1
36	GO:1903725	BP	regulation of phospholipid metabolic process	90	1	0.0237582	1
37	GO:0046890	BP	regulation of lipid biosynthetic process	197	1	0.0338788	1
38	GO:0060041	BP	retina development in camera-type eye	147	1	0.0369490	1
39	GO:0046474	BP	glycerophospholipid biosynthetic process	218	1	0.0376870	1
40	GO:0045732	BP	positive regulation of protein catabolic process	209	1	0.0380340	1
41	GO:0008654	BP	phospholipid biosynthetic process	259	1	0.0413918	1
42	GO:0045017	BP	glycerolipid biosynthetic process	251	1	0.0431814	1
43	GO:0030667	CC	secretory granule membrane	292	1	0.0436461	1
44	GO:0001894	BP	tissue homeostasis	246	1	0.0447369	1
45	GO:0005765	CC	lysosomal membrane	353	1	0.0484312	1
46	GO:0098852	CC	lytic vacuole membrane	353	1	0.0484312	1
NA	NA	NA	NA	NA	NA	NA	NA
NA.1	NA	NA	NA	NA	NA	NA	NA
NA.2	NA	NA	NA	NA	NA	NA	NA
NA.3	NA	NA	NA	NA	NA	NA	NA
NA.4	NA	NA	NA	NA	NA	NA	NA
NA.5	NA	NA	NA	NA	NA	NA	NA
NA.6	NA	NA	NA	NA	NA	NA	NA
NA.7	NA	NA	NA	NA	NA	NA	NA
NA.8	NA	NA	NA	NA	NA	NA	NA
NA.9	NA	NA	NA	NA	NA	NA	NA
NA.10	NA	NA	NA	NA	NA	NA	NA
NA.11	NA	NA	NA	NA	NA	NA	NA
NA.12	NA	NA	NA	NA	NA	NA	NA
NA.13	NA	NA	NA	NA	NA	NA	NA
NA.14	NA	NA	NA	NA	NA	NA	NA
NA.15	NA	NA	NA	NA	NA	NA	NA
NA.16	NA	NA	NA	NA	NA	NA	NA
NA.17	NA	NA	NA	NA	NA	NA	NA
NA.18	NA	NA	NA	NA	NA	NA	NA
NA.19	NA	NA	NA	NA	NA	NA	NA
NA.20	NA	NA	NA	NA	NA	NA	NA
NA.21	NA	NA	NA	NA	NA	NA	NA
NA.22	NA	NA	NA	NA	NA	NA	NA
NA.23	NA	NA	NA	NA	NA	NA	NA
NA.24	NA	NA	NA	NA	NA	NA	NA
NA.25	NA	NA	NA	NA	NA	NA	NA
NA.26	NA	NA	NA	NA	NA	NA	NA
NA.27	NA	NA	NA	NA	NA	NA	NA
NA.28	NA	NA	NA	NA	NA	NA	NA
NA.29	NA	NA	NA	NA	NA	NA	NA
NA.30	NA	NA	NA	NA	NA	NA	NA
NA.31	NA	NA	NA	NA	NA	NA	NA
NA.32	NA	NA	NA	NA	NA	NA	NA
NA.33	NA	NA	NA	NA	NA	NA	NA
NA.34	NA	NA	NA	NA	NA	NA	NA
NA.35	NA	NA	NA	NA	NA	NA	NA
NA.36	NA	NA	NA	NA	NA	NA	NA
NA.37	NA	NA	NA	NA	NA	NA	NA
NA.38	NA	NA	NA	NA	NA	NA	NA
NA.39	NA	NA	NA	NA	NA	NA	NA
NA.40	NA	NA	NA	NA	NA	NA	NA
NA.41	NA	NA	NA	NA	NA	NA	NA
NA.42	NA	NA	NA	NA	NA	NA	NA
NA.43	NA	NA	NA	NA	NA	NA	NA
NA.44	NA	NA	NA	NA	NA	NA	NA
NA.45	NA	NA	NA	NA	NA	NA	NA
NA.46	NA	NA	NA	NA	NA	NA	NA
NA.47	NA	NA	NA	NA	NA	NA	NA
NA.48	NA	NA	NA	NA	NA	NA	NA
NA.49	NA	NA	NA	NA	NA	NA	NA
NA.50	NA	NA	NA	NA	NA	NA	NA
NA.51	NA	NA	NA	NA	NA	NA	NA
NA.52	NA	NA	NA	NA	NA	NA	NA
NA.53	NA	NA	NA	NA	NA	NA	NA

With cell type adjustment

Blood only

metal_blood_cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_1204201.tbl', sep = "\t")

metal_blood_cell = metalProcess(metal_blood_cell)

write.csv(metal_blood_cell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_blood_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_blood_cell$P.value < 0.05)
#  FALSE   TRUE 
# 353990  23361 

# FDR
table(metal_blood_cell$P.FDR < 0.05)
#  FALSE   TRUE 
# 377350      1 

table(metal_blood_cell$P.FDR < 0.1)
#  FALSE   TRUE 
# 377343      8

# Bonferroni
table(metal_blood_cell$P.Bonf < 0.05)
#  FALSE   TRUE 
#  377350      1 


# GO analysis, nominally-significant probes

go_metal_blood_cell = gometh(sig.cpg = metal_blood_cell$Name[metal_blood_cell$P.FDR < 0.1], all.cpg = metal_blood_cell$Name, array.type = '450K', sig.genes = T, anno = annAll2)
go_metal_blood_cell = go_metal_blood_cell[order(go_metal_blood_cell$P.DE),]

table(go_metal_blood_cell$P.DE<0.05)
# FALSE  TRUE 
# 22131   452

table(go_metal_blood_cell$FDR<0.05)
# FALSE 
# 22583 

write.csv(go_metal_blood_cell[go_metal_blood_cell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DMP_blood_cell_common_120420.csv')


# KEGG analysis, nominally-significant probes

kegg_metal_blood_cell = gometh(sig.cpg = metal_blood_cell$Name[metal_blood_cell$P.FDR < 0.1], all.cpg = metal_blood_cell$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_blood_cell = kegg_metal_blood_cell[order(kegg_metal_blood_cell$P.DE),]

table(kegg_metal_blood_cell$P.DE<0.05)
# FALSE  TRUE 
# 337     3 

table(kegg_metal_blood_cell$FDR<0.05)
# FALSE 
  # 340

write.csv(kegg_metal_blood_cell[c(1:20),], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DMP_blood_cell_common_120420.csv')



# Plotting

gg_qqplot(metal_blood_cell$P.value)
quartz.save('qq_metal_blood_cell_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_blood_cell)
quartz.save('manhattan_metal_blood_cell_120420.png', type = "png", dpi = 300)

volcano_meta(metal_blood_cell)
quartz.save('volcano_metal_blood_cell_120420.png', type = "png", dpi = 300)

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_cell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_cell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_cell_120420.png")

Top 100 probes

X	Name	Effect	StdErr	P.value	Direction	P.FDR	P.Bonf	chr	pos	UCSC_RefGene_Name	UCSC_RefGene_Group
194923	cg13490635	0.3069	0.0567	1.00e-07	+++	0.0237656	0.0237656	chr8	30242021	RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS	5’UTR;5’UTR;1stExon;1stExon;1stExon;5’UTR;1stExon;5’UTR
186512	cg12835806	-0.2055	0.0408	5.00e-07	—	0.0861304	0.1819964	chr16	2812435	SRRM2	Body
143925	cg09595163	0.5056	0.1019	7.00e-07	+++	0.0861304	0.2655796	chr3	55515541	WNT5A	Body
360597	cg26412543	-0.2648	0.0540	1.00e-06	—	0.0861304	0.3598419	chr6	32128829	PPT2;PPT2	Body;Body
44706	cg02799448	0.1687	0.0351	1.50e-06	-++	0.0861304	0.5607436	chr6	137817008	OLIG3	TSS1500
95521	cg06218338	0.3073	0.0641	1.60e-06	-++	0.0861304	0.6181009	chr7	27231894
353232	cg25840057	-0.1794	0.0375	1.70e-06	+–	0.0861304	0.6456476	chr13	113730354	MCF2L;MCF2L	Body;Body
220977	cg15206981	-0.2178	0.0456	1.80e-06	—	0.0861304	0.6890429	chr4	124323013	SPRY1;SPRY1	Body;Body
30961	cg01927825	-0.3417	0.0725	2.50e-06	—	0.1032265	0.9290382	chr1	2121724	C1orf86;LOC100128003;C1orf86	Body;Body;Body
222521	cg15345437	-0.1694	0.0362	2.90e-06	—	0.1046133	1.0000000	chr11	62620843	SNORD22;SNORD31;SNHG1	TSS1500;Body;Body
201470	cg13900348	0.3509	0.0755	3.40e-06	+++	0.1046133	1.0000000	chr5	76114646	F2RL1	TSS200
20130	cg01218206	-0.2163	0.0467	3.60e-06	—	0.1046133	1.0000000	chr11	116933977	SIK3	Body
286295	cg20380069	0.1757	0.0379	3.60e-06	+++	0.1046133	1.0000000	chr12	120806617	MSI1	Body
2859	cg00160440	-0.1362	0.0297	4.50e-06	—	0.1202402	1.0000000	chr4	134077575	PCDH10	Body
64145	cg04080022	-0.1951	0.0430	5.80e-06	—	0.1363416	1.0000000	chr16	89648534	CPNE7;CPNE7	Body;Body
96670	cg06313349	-0.2251	0.0496	5.80e-06	—	0.1363416	1.0000000	chr7	157494424	PTPRN2;PTPRN2;PTPRN2	Body;Body;Body
173665	cg11832210	0.4809	0.1069	6.80e-06	+++	0.1513178	1.0000000	chr10	91295346	SLC16A12	TSS200
48278	cg03025061	-0.1950	0.0437	8.00e-06	—	0.1566950	1.0000000	chr8	109261275	EIF3E	TSS1500
184123	cg12637057	0.2537	0.0569	8.10e-06	+++	0.1566950	1.0000000	chr20	59967284	CDH4	Body
145527	cg09714379	0.2894	0.0649	8.30e-06	+++	0.1566950	1.0000000	chr10	135044040	UTF1	1stExon
35348	cg02206980	-0.5285	0.1199	1.04e-05	—	0.1855881	1.0000000	chr6	13574034	SIRT5;SIRT5	TSS1500;TSS1500
176796	cg12065616	-0.1729	0.0393	1.08e-05	—	0.1855881	1.0000000	chr12	94954828
61580	cg03906434	0.3445	0.0794	1.45e-05	-++	0.2168360	1.0000000	chr7	27231819
114412	cg07492924	-0.3742	0.0863	1.47e-05	—	0.2168360	1.0000000	chr16	433825	LOC100134368	Body
291217	cg20784693	-0.5836	0.1347	1.47e-05	—	0.2168360	1.0000000	chr2	239984030	HDAC4	Body
85525	cg05507514	-0.1798	0.0416	1.55e-05	—	0.2168360	1.0000000	chr3	153842846	SGEF	Body
50150	cg03149958	-0.1844	0.0427	1.58e-05	—	0.2168360	1.0000000	chr6	36326677
279928	cg19851029	0.1962	0.0456	1.68e-05	+++	0.2168360	1.0000000	chr3	138669137	C3orf72	Body
178323	cg12174276	0.1279	0.0297	1.69e-05	+++	0.2168360	1.0000000	chr6	166401921	LOC441177;C6orf176;C6orf176	Body;TSS1500;TSS1500
200512	cg13837335	-0.1365	0.0319	1.81e-05	—	0.2168360	1.0000000	chr9	2191798	SMARCA2;SMARCA2	Body;Body
133800	cg08856347	0.2545	0.0596	1.94e-05	+++	0.2168360	1.0000000	chr2	289390	FAM150B	TSS1500
187357	cg12908187	0.1873	0.0439	1.94e-05	-++	0.2168360	1.0000000	chr16	88450261
373928	cg27406919	-0.1801	0.0422	1.95e-05	—	0.2168360	1.0000000	chr16	87212733
201996	cg13928490	-0.2502	0.0586	1.95e-05	—	0.2168360	1.0000000	chr13	51640442	GUCY1B2	TSS200
46686	cg02925222	0.1116	0.0264	2.29e-05	+++	0.2168360	1.0000000	chr11	280445	NLRP6	Body
92037	cg05965902	0.1887	0.0446	2.31e-05	+++	0.2168360	1.0000000	chr13	21635727	LATS2	TSS200
23933	cg01464730	-0.7699	0.1821	2.35e-05	—	0.2168360	1.0000000	chr17	78809873	RPTOR;RPTOR	Body;Body
168281	cg11414610	-0.1493	0.0353	2.38e-05	—	0.2168360	1.0000000	chr19	16528319	EPS15L1	Body
254158	cg17819053	0.1555	0.0368	2.38e-05	+++	0.2168360	1.0000000	chr1	119549626
347007	cg25330878	-0.1506	0.0357	2.48e-05	—	0.2168360	1.0000000	chr17	17379109	MED9	TSS1500
131753	cg08706492	0.2375	0.0564	2.57e-05	+++	0.2168360	1.0000000	chr1	247374357
4731	cg00284153	-0.1746	0.0415	2.57e-05	—	0.2168360	1.0000000	chr10	135171713	C10orf125;C10orf125	TSS200;TSS200
306721	cg22111078	0.4708	0.1119	2.60e-05	+++	0.2168360	1.0000000	chr5	172655925
198286	cg13692433	0.1821	0.0433	2.65e-05	+++	0.2168360	1.0000000	chr11	112832159	NCAM1;NCAM1;NCAM1;NCAM1;NCAM1;NCAM1	1stExon;5’UTR;5’UTR;1stExon;5’UTR;1stExon
282053	cg20011402	0.3952	0.0941	2.66e-05	+++	0.2168360	1.0000000	chr10	17496239	ST8SIA6	1stExon
236494	cg16427033	-0.1492	0.0355	2.70e-05	+–	0.2168360	1.0000000	chr10	109023583
363371	cg26623444	0.1747	0.0416	2.73e-05	+++	0.2168360	1.0000000	chr7	31376092
228619	cg15830431	0.1666	0.0398	2.78e-05	++-	0.2168360	1.0000000	chr8	99952591
166619	cg11289100	0.2363	0.0565	2.86e-05	+++	0.2168360	1.0000000	chr17	19313024	RNF112	TSS1500
199780	cg13791254	0.5591	0.1338	2.93e-05	-++	0.2168360	1.0000000	chr9	100616607	FOXE1	1stExon
321357	cg23300529	-0.1586	0.0380	3.01e-05	—	0.2168360	1.0000000	chr8	21989012	HR;HR	TSS1500;TSS1500
353248	cg25840780	-0.3055	0.0733	3.12e-05	—	0.2168360	1.0000000	chr20	50156843	NFATC2;NFATC2;NFATC2	Body;Body;Body
193620	cg13415566	-0.3939	0.0947	3.18e-05	—	0.2168360	1.0000000	chr10	125423240
295061	cg21122375	-0.2285	0.0550	3.22e-05	—	0.2168360	1.0000000	chr7	37956869	SFRP4	TSS1500
312496	cg22621867	0.3367	0.0811	3.27e-05	+++	0.2168360	1.0000000	chr3	51990301	GPR62	1stExon
291688	cg20824761	0.5956	0.1434	3.28e-05	+++	0.2168360	1.0000000	chr15	69591567	PAQR5	5’UTR
250912	cg17523124	0.1690	0.0408	3.40e-05	+++	0.2168360	1.0000000	chr20	24451769	TMEM90B	5’UTR
304218	cg21885638	-0.1303	0.0315	3.45e-05	—	0.2168360	1.0000000	chr3	129306552	PLXND1	Body
72911	cg04658543	0.2106	0.0509	3.51e-05	+++	0.2168360	1.0000000	chr12	113904848	LHX5	Body
118338	cg07766612	0.4675	0.1131	3.57e-05	+++	0.2168360	1.0000000	chr1	26372887	SLC30A2;SLC30A2	TSS1500;TSS1500
265230	cg18672986	0.3001	0.0727	3.66e-05	+++	0.2168360	1.0000000	chr19	35521772	SCN1B;SCN1B	Body;Body
110684	cg07232688	-0.1766	0.0428	3.66e-05	—	0.2168360	1.0000000	chr1	100644688	LRRC39	TSS1500
316250	cg22915154	-0.2157	0.0523	3.69e-05	—	0.2168360	1.0000000	chr11	68816030	TPCN2	TSS1500
292390	cg20899625	-0.1458	0.0354	3.78e-05	—	0.2168360	1.0000000	chr3	126721131	PLXNA1	Body
180848	cg12392225	-0.1565	0.0380	3.79e-05	—	0.2168360	1.0000000	chr2	3464066	TTC15	Body
86791	cg05600350	0.4214	0.1023	3.82e-05	+++	0.2168360	1.0000000	chr4	4858598
295936	cg21185289	0.4583	0.1113	3.85e-05	+++	0.2168360	1.0000000	chr2	74743437	TLX2	3’UTR
225228	cg15572907	0.4958	0.1206	3.97e-05	+++	0.2171135	1.0000000	chr19	40995921	SPTBN4	Body
354980	cg25996001	-0.1629	0.0396	3.97e-05	—	0.2171135	1.0000000	chr15	23003087	CYFIP1;CYFIP1	3’UTR;3’UTR
73319	cg04685632	-0.1611	0.0393	4.15e-05	—	0.2178127	1.0000000	chr20	62082611	KCNQ2;KCNQ2;KCNQ2;KCNQ2;KCNQ2	Body;Body;Body;Body;Body
343981	cg25076597	-0.3534	0.0862	4.15e-05	—	0.2178127	1.0000000	chr10	134150581	LRRC27;LRRC27;LRRC27;LRRC27;LRRC27	Body;TSS200;Body;Body;Body
90057	cg05837401	0.2287	0.0558	4.17e-05	+++	0.2178127	1.0000000	chr3	125899086	ALDH1L1	5’UTR
5363	cg00321074	-0.1290	0.0316	4.41e-05	—	0.2178127	1.0000000	chr3	19990693	RAB5A	5’UTR
136595	cg09064848	0.2053	0.0503	4.41e-05	+++	0.2178127	1.0000000	chr17	3627007	ITGAE;GSG2	Body;TSS200
219413	cg15083775	0.1410	0.0345	4.42e-05	–+	0.2178127	1.0000000	chr17	48054048
297867	cg21344215	0.1552	0.0380	4.47e-05	+++	0.2178127	1.0000000	chr2	27851972	GPN1;CCDC121;CCDC121;GPN1;CCDC121;GPN1;GPN1;GPN1	5’UTR;TSS1500;TSS200;Body;TSS1500;5’UTR;Body;1stExon
5575	cg00333154	0.3250	0.0797	4.53e-05	+++	0.2178127	1.0000000	chr6	106808703
2422	cg00133970	-0.2104	0.0516	4.56e-05	—	0.2178127	1.0000000	chr7	44123200	POLM	TSS1500
214534	cg14709833	0.3309	0.0812	4.56e-05	+++	0.2178127	1.0000000	chr13	112157732
34800	cg02166532	0.1862	0.0457	4.68e-05	+++	0.2207503	1.0000000	chr11	2159853	INS-IGF2;IGF2;IGF2;IGF2;IGF2	Body;Body;5’UTR;5’UTR;1stExon
260043	cg18259339	-0.2166	0.0534	4.96e-05	—	0.2260924	1.0000000	chr17	76441793	DNAH17	Body
168429	cg11425470	-0.1835	0.0452	4.97e-05	—	0.2260924	1.0000000	chr1	109271795	FNDC7	Body
324549	cg23558842	0.3088	0.0761	4.97e-05	+++	0.2260924	1.0000000	chr11	15095178	CALCB;CALCB	1stExon;5’UTR
331371	cg24090911	-0.2089	0.0516	5.13e-05	—	0.2273111	1.0000000	chr5	400732	AHRR	Body
180577	cg12368188	0.3807	0.0941	5.17e-05	+++	0.2273111	1.0000000	chr15	67326082
93	cg00004257	0.2348	0.0580	5.19e-05	+++	0.2273111	1.0000000	chr1	34629175	CSMD2	Body
18568	cg01117452	-0.1664	0.0412	5.27e-05	—	0.2273111	1.0000000	chr14	72703626	RGS6	Body
307232	cg22153116	0.1627	0.0402	5.30e-05	-++	0.2273111	1.0000000	chr9	15306736	TTC39B;TTC39B;TTC39B;TTC39B	Body;Body;Body;Body
351351	cg25687423	-0.1654	0.0412	5.82e-05	—	0.2419608	1.0000000	chr6	43193521	C6orf108;C6orf108	Body;3’UTR
301289	cg21629895	-0.1786	0.0444	5.82e-05	—	0.2419608	1.0000000	chr2	25565795	DNMT3A;DNMT3A;DNMT3A	TSS1500;TSS1500;TSS1500
153656	cg10308749	-0.3923	0.0976	5.84e-05	—	0.2419608	1.0000000	chr6	126080335	HEY2	Body
199878	cg13797073	-0.2046	0.0509	5.93e-05	—	0.2431043	1.0000000	chr9	71199964
139515	cg09275980	0.3030	0.0755	6.04e-05	+++	0.2449941	1.0000000	chr15	25350925	SNORD116-29	TSS1500
184603	cg12673019	-0.1488	0.0371	6.12e-05	+–	0.2458402	1.0000000	chr11	17939679	SERGEF	Body
100076	cg06555468	0.2055	0.0514	6.28e-05	+++	0.2481358	1.0000000	chr7	2094790	MAD1L1;MAD1L1;MAD1L1	Body;Body;Body
309222	cg22332910	0.2330	0.0582	6.34e-05	+++	0.2481358	1.0000000	chr11	35641226	FJX1	1stExon
157910	cg10615519	0.4241	0.1061	6.42e-05	+++	0.2481358	1.0000000	chr12	88974243	KITLG;KITLG	TSS200;TSS200
116539	cg07636145	-0.2033	0.0509	6.45e-05	—	0.2481358	1.0000000	chr16	56228188	DKFZP434H168;GNAO1;GNAO1	Body;Body;Body
131348	cg08680083	-0.2311	0.0579	6.64e-05	—	0.2481358	1.0000000	chr19	50309143	AP2A1;AP2A1	Body;Body
16383	cg00990385	-0.1788	0.0448	6.70e-05	—	0.2481358	1.0000000	chr12	113587690	CCDC42B	1stExon

---

Top 100 GO terms

X	ONTOLOGY	TERM	N	DE	P.DE	FDR	SigGenesInSet
GO:0000132	BP	establishment of mitotic spindle orientation	30	1	0.0170717	1	SPRY1
GO:0000578	BP	embryonic axis specification	36	1	0.0241637	1	WNT5A
GO:0000932	CC	P-body	86	1	0.0416833	1	RBPMS
GO:0001654	BP	eye development	373	2	0.0283476	1	SPRY1,WNT5A
GO:0001655	BP	urogenital system development	320	2	0.0204470	1	SPRY1,WNT5A
GO:0001702	BP	gastrulation with mouth forming second	26	1	0.0205125	1	WNT5A
GO:0001708	BP	cell fate specification	99	2	0.0032883	1	OLIG3,WNT5A
GO:0001756	BP	somitogenesis	67	1	0.0478998	1	WNT5A
GO:0001759	BP	organ induction	23	2	0.0002145	1	SPRY1,WNT5A
GO:0001763	BP	morphogenesis of a branching structure	195	2	0.0110409	1	SPRY1,WNT5A
GO:0001837	BP	epithelial to mesenchymal transition	147	2	0.0044294	1	SPRY1,WNT5A
GO:0001932	BP	regulation of protein phosphorylation	1405	3	0.0316030	1	SPRY1,RBPMS,WNT5A
GO:0001947	BP	heart looping	62	1	0.0402549	1	WNT5A
GO:0001961	BP	positive regulation of cytokine-mediated signaling pathway	49	1	0.0147355	1	WNT5A
GO:0002011	BP	morphogenesis of an epithelial sheet	56	1	0.0451227	1	WNT5A
GO:0002053	BP	positive regulation of mesenchymal cell proliferation	25	1	0.0307164	1	WNT5A
GO:0002066	BP	columnar/cuboidal epithelial cell development	62	1	0.0434813	1	WNT5A
GO:0002067	BP	glandular epithelial cell differentiation	48	1	0.0425664	1	WNT5A
GO:0002068	BP	glandular epithelial cell development	26	1	0.0248938	1	WNT5A
GO:0002072	BP	optic cup morphogenesis involved in camera-type eye development	8	1	0.0105911	1	WNT5A
GO:0002088	BP	lens development in camera-type eye	80	2	0.0011900	1	SPRY1,WNT5A
GO:0002367	BP	cytokine production involved in immune response	94	1	0.0371153	1	WNT5A
GO:0002687	BP	positive regulation of leukocyte migration	131	1	0.0435196	1	WNT5A
GO:0002688	BP	regulation of leukocyte chemotaxis	112	1	0.0390771	1	WNT5A
GO:0002690	BP	positive regulation of leukocyte chemotaxis	89	1	0.0297444	1	WNT5A
GO:0002700	BP	regulation of production of molecular mediator of immune response	130	1	0.0466534	1	WNT5A
GO:0002702	BP	positive regulation of production of molecular mediator of immune response	93	1	0.0320167	1	WNT5A
GO:0002718	BP	regulation of cytokine production involved in immune response	74	1	0.0341841	1	WNT5A
GO:0002720	BP	positive regulation of cytokine production involved in immune response	50	1	0.0216393	1	WNT5A
GO:0003002	BP	regionalization	343	2	0.0280862	1	SPRY1,WNT5A
GO:0003007	BP	heart morphogenesis	255	2	0.0147387	1	SPRY1,WNT5A
GO:0003128	BP	heart field specification	17	1	0.0197641	1	WNT5A
GO:0003129	BP	heart induction	10	1	0.0112860	1	WNT5A
GO:0003138	BP	primary heart field specification	3	1	0.0039931	1	WNT5A
GO:0003139	BP	secondary heart field specification	11	1	0.0124197	1	WNT5A
GO:0003143	BP	embryonic heart tube morphogenesis	68	1	0.0462131	1	WNT5A
GO:0003156	BP	regulation of animal organ formation	37	2	0.0006690	1	SPRY1,WNT5A
GO:0003209	BP	cardiac atrium morphogenesis	30	1	0.0274007	1	WNT5A
GO:0003213	BP	cardiac right atrium morphogenesis	2	1	0.0041147	1	WNT5A
GO:0003230	BP	cardiac atrium development	36	1	0.0298481	1	WNT5A
GO:0003283	BP	atrial septum development	23	1	0.0203575	1	WNT5A
GO:0003306	BP	Wnt signaling pathway involved in heart development	13	1	0.0077832	1	WNT5A
GO:0003307	BP	regulation of Wnt signaling pathway involved in heart development	9	1	0.0048594	1	WNT5A
GO:0003308	BP	negative regulation of Wnt signaling pathway involved in heart development	7	1	0.0033385	1	WNT5A
GO:0003309	BP	type B pancreatic cell differentiation	25	1	0.0221791	1	WNT5A
GO:0003323	BP	type B pancreatic cell development	20	1	0.0159645	1	WNT5A
GO:0003344	BP	pericardium morphogenesis	9	1	0.0086510	1	WNT5A
GO:0003401	BP	axis elongation	28	2	0.0003656	1	SPRY1,WNT5A
GO:0003402	BP	planar cell polarity pathway involved in axis elongation	6	1	0.0093298	1	WNT5A
GO:0003408	BP	optic cup formation involved in camera-type eye development	3	1	0.0040144	1	WNT5A
GO:0003712	MF	transcription coregulator activity	462	2	0.0239655	1	RBPMS,OLIG3
GO:0003727	MF	single-stranded RNA binding	81	1	0.0376670	1	RBPMS
GO:0003729	MF	mRNA binding	491	2	0.0054702	1	RBPMS,SRRM2
GO:0005109	MF	frizzled binding	37	1	0.0306569	1	WNT5A
GO:0005115	MF	receptor tyrosine kinase-like orphan receptor binding	1	1	0.0020187	1	WNT5A
GO:0005543	MF	phospholipid binding	425	2	0.0226882	1	MCF2L,WNT5A
GO:0005681	CC	spliceosomal complex	177	1	0.0442644	1	SRRM2
GO:0005684	CC	U2-type spliceosomal complex	88	1	0.0244405	1	SRRM2
GO:0006139	BP	nucleobase-containing compound metabolic process	5578	5	0.0385323	1	RBPMS,OLIG3,SRRM2,WNT5A,PPT2
GO:0006396	BP	RNA processing	1235	2	0.0261175	1	RBPMS,SRRM2
GO:0006582	BP	melanin metabolic process	22	1	0.0137342	1	WNT5A
GO:0006637	BP	acyl-CoA metabolic process	95	1	0.0343804	1	PPT2
GO:0006725	BP	cellular aromatic compound metabolic process	5786	5	0.0436372	1	RBPMS,OLIG3,SRRM2,WNT5A,PPT2
GO:0006793	BP	phosphorus metabolic process	3152	4	0.0465551	1	SPRY1,RBPMS,WNT5A,PPT2
GO:0006796	BP	phosphate-containing compound metabolic process	3127	4	0.0453948	1	SPRY1,RBPMS,WNT5A,PPT2
GO:0007163	BP	establishment or maintenance of cell polarity	214	2	0.0091182	1	SPRY1,WNT5A
GO:0007167	BP	enzyme linked receptor protein signaling pathway	1029	3	0.0217499	1	SPRY1,RBPMS,WNT5A
GO:0007178	BP	transmembrane receptor protein serine/threonine kinase signaling pathway	341	3	0.0012016	1	SPRY1,RBPMS,WNT5A
GO:0007223	BP	Wnt signaling pathway, calcium modulating pathway	38	1	0.0289937	1	WNT5A
GO:0007257	BP	activation of JUN kinase activity	38	1	0.0243513	1	WNT5A
GO:0007264	BP	small GTPase mediated signal transduction	469	2	0.0393178	1	SPRY1,MCF2L
GO:0007350	BP	blastoderm segmentation	20	1	0.0186601	1	WNT5A
GO:0007351	BP	tripartite regional subdivision	16	1	0.0140401	1	WNT5A
GO:0007389	BP	pattern specification process	436	2	0.0405926	1	SPRY1,WNT5A
GO:0007442	BP	hindgut morphogenesis	7	1	0.0094349	1	WNT5A
GO:0007494	BP	midgut development	12	1	0.0125057	1	WNT5A
GO:0008143	MF	poly(A) binding	21	1	0.0095053	1	RBPMS
GO:0008474	MF	palmitoyl-(protein) hydrolase activity	13	1	0.0047432	1	PPT2
GO:0008543	BP	fibroblast growth factor receptor signaling pathway	112	2	0.0021005	1	SPRY1,WNT5A
GO:0008595	BP	anterior/posterior axis specification, embryo	16	1	0.0140401	1	WNT5A
GO:0009948	BP	anterior/posterior axis specification	48	1	0.0317891	1	WNT5A
GO:0010092	BP	specification of animal organ identity	35	2	0.0006903	1	SPRY1,WNT5A
GO:0010453	BP	regulation of cell fate commitment	37	1	0.0217979	1	WNT5A
GO:0010463	BP	mesenchymal cell proliferation	43	1	0.0467404	1	WNT5A
GO:0010464	BP	regulation of mesenchymal cell proliferation	33	1	0.0385379	1	WNT5A
GO:0010494	CC	cytoplasmic stress granule	69	1	0.0263234	1	RBPMS
GO:0010719	BP	negative regulation of epithelial to mesenchymal transition	40	1	0.0284573	1	SPRY1
GO:0010799	BP	regulation of peptidyl-threonine phosphorylation	46	1	0.0307112	1	WNT5A
GO:0010800	BP	positive regulation of peptidyl-threonine phosphorylation	28	1	0.0185498	1	WNT5A
GO:0010818	BP	T cell chemotaxis	22	1	0.0071995	1	WNT5A
GO:0010819	BP	regulation of T cell chemotaxis	15	1	0.0049580	1	WNT5A
GO:0010820	BP	positive regulation of T cell chemotaxis	14	1	0.0049580	1	WNT5A
GO:0010862	BP	positive regulation of pathway-restricted SMAD protein phosphorylation	47	1	0.0192732	1	RBPMS
GO:0010934	BP	macrophage cytokine production	15	1	0.0081533	1	WNT5A
GO:0010935	BP	regulation of macrophage cytokine production	14	1	0.0078638	1	WNT5A
GO:0015030	CC	Cajal body	70	1	0.0124663	1	SRRM2
GO:0016790	MF	thiolester hydrolase activity	38	1	0.0128339	1	PPT2
GO:0019748	BP	secondary metabolic process	55	1	0.0252502	1	WNT5A
GO:0021517	BP	ventral spinal cord development	48	1	0.0444256	1	OLIG3
GO:0021520	BP	spinal cord motor neuron cell fate specification	13	1	0.0173372	1	OLIG3

Including buccal

metal_all_cell = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_1204201.tbl', sep = "\t")

metal_all_cell = metalProcess(metal_all_cell)

write.csv(metal_all_cell, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DMP_all_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_all_cell$P.value < 0.05)
#  FALSE   TRUE 
# 354739  22612

# FDR
table(metal_all_cell$P.FDR < 0.05)
# FALSE   TRUE 
# 377348      3 

table(metal_all_cell$P.FDR < 0.1)
# FALSE   TRUE 
# 377326     25 

# Bonferroni
table(metal_all_cell$P.Bonf < 0.05)
# FALSE 
# 377351 


# GO analysis, nominally-significant probes

go_metal_all_cell = gometh(sig.cpg = metal_all_cell$Name[metal_all_cell$P.FDR < 0.1], all.cpg = metal_all_cell$Name, array.type = '450K', anno = annAll2)
go_metal_all_cell = go_metal_all_cell[order(go_metal_all_cell$P.DE),]

table(go_metal_all_cell$P.DE<0.05)
# FALSE  TRUE 
# 22246   337

table(go_metal_all_cell$FDR<0.05)
# FALSE 
# 22583 

write.csv(go_metal_all_cell[go_metal_all_cell$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DMP_all_cell_common_120420.csv')


# KEGG analysis, nominally-significant probes

kegg_metal_all_cell = gometh(sig.cpg = metal_all_cell$Name[metal_all_cell$P.FDR < 0.1], all.cpg = metal_all_cell$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_all_cell = kegg_metal_all_cell[order(kegg_metal_all_cell$P.DE),]

table(kegg_metal_all_cell$P.DE<0.05)
# FALSE  TRUE 
# 335     5 

table(kegg_metal_all_cell$FDR<0.05)
# FALSE 
# 340

write.csv(kegg_metal_all_cell[c(1:20),], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DMP_all_cell_common_120420.csv')



# Plotting

gg_qqplot(metal_all_cell$P.value)
quartz.save('qq_metal_all_cell_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_all_cell, FDR=T)
quartz.save('manhattan_metal_all_cell_120420.png', type = "png", dpi = 300)

volcano_meta(metal_all_cell)
quartz.save('volcano_metal_all_cell_120420.png', type = "png", dpi = 300)

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_cell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_cell_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_cell_120420.png")

Top 100 probes

X	Name	Effect	StdErr	P.value	Direction	P.FDR	P.Bonf	chr	pos	UCSC_RefGene_Name	UCSC_RefGene_Group
139515	cg09275980	0.3064	0.0594	3.00e-07	++++	0.0415715	0.0950925	chr15	25350925	SNORD116-29	TSS1500
291217	cg20784693	-0.6410	0.1252	3.00e-07	—-	0.0415715	0.1162996	chr2	239984030	HDAC4	Body
260100	cg18263451	-0.1213	0.0238	3.00e-07	–+-	0.0415715	0.1247145	chr1	25573180	C1orf63	Body
254158	cg17819053	0.1723	0.0348	7.00e-07	++++	0.0603460	0.2826736	chr1	119549626
95521	cg06218338	0.3110	0.0630	8.00e-07	-+++	0.0603460	0.3017299	chr7	27231894
284743	cg20247661	0.1739	0.0356	1.00e-06	-+++	0.0633950	0.3890489	chr10	21812368	C10orf140	5’UTR
184123	cg12637057	0.2531	0.0521	1.20e-06	++++	0.0633950	0.4437648	chr20	59967284	CDH4	Body
46686	cg02925222	0.1166	0.0242	1.40e-06	++++	0.0637723	0.5305555	chr11	280445	NLRP6	Body
90057	cg05837401	0.2379	0.0496	1.60e-06	++++	0.0637723	0.6052710	chr3	125899086	ALDH1L1	5’UTR
222521	cg15345437	-0.1530	0.0320	1.70e-06	—-	0.0637723	0.6377232	chr11	62620843	SNORD22;SNORD31;SNHG1	TSS1500;Body;Body
114412	cg07492924	-0.3734	0.0791	2.40e-06	—-	0.0810276	0.8913031	chr16	433825	LOC100134368	Body
143925	cg09595163	0.4584	0.0977	2.70e-06	+++-	0.0832204	1.0000000	chr3	55515541	WNT5A	Body
44706	cg02799448	0.1600	0.0342	2.90e-06	-++-	0.0832204	1.0000000	chr6	137817008	OLIG3	TSS1500
194923	cg13490635	0.2316	0.0500	3.50e-06	+++-	0.0931114	1.0000000	chr8	30242021	RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS;RBPMS	5’UTR;5’UTR;1stExon;1stExon;1stExon;5’UTR;1stExon;5’UTR
225228	cg15572907	0.5107	0.1105	3.80e-06	++++	0.0931114	1.0000000	chr19	40995921	SPTBN4	Body
9270	cg00550554	-0.1879	0.0407	3.90e-06	—-	0.0931114	1.0000000	chr6	30294969	HCG18;TRIM39;HCG18;TRIM39	TSS200;5’UTR;TSS200;TSS200
138010	cg09169455	-0.4663	0.1015	4.30e-06	—-	0.0953755	1.0000000	chr5	16843340	MYO10	Body
360597	cg26412543	-0.2220	0.0485	4.70e-06	—-	0.0953755	1.0000000	chr6	32128829	PPT2;PPT2	Body;Body
363371	cg26623444	0.1849	0.0406	5.10e-06	++++	0.0953755	1.0000000	chr7	31376092
30961	cg01927825	-0.2978	0.0654	5.30e-06	—-	0.0953755	1.0000000	chr1	2121724	C1orf86;LOC100128003;C1orf86	Body;Body;Body
343981	cg25076597	-0.3140	0.0690	5.40e-06	—-	0.0953755	1.0000000	chr10	134150581	LRRC27;LRRC27;LRRC27;LRRC27;LRRC27	Body;TSS200;Body;Body;Body
23933	cg01464730	-0.7679	0.1692	5.60e-06	—-	0.0953755	1.0000000	chr17	78809873	RPTOR;RPTOR	Body;Body
136234	cg09035938	0.1847	0.0408	6.00e-06	++++	0.0953755	1.0000000	chr1	35347799	DLGAP3	Body
33505	cg02081266	0.3474	0.0768	6.10e-06	++++	0.0953755	1.0000000	chr17	59529618
277060	cg19640581	-0.2875	0.0638	6.50e-06	—-	0.0977943	1.0000000	chr5	501343	SLC9A3	Body
61580	cg03906434	0.3385	0.0755	7.30e-06	-+++	0.1050131	1.0000000	chr7	27231819
299146	cg21468180	-0.1345	0.0301	7.80e-06	—-	0.1050131	1.0000000	chr3	13697288	LOC285375	Body
243179	cg16919449	-0.4103	0.0919	8.10e-06	—-	0.1050131	1.0000000	chr10	36054185
373928	cg27406919	-0.1775	0.0399	8.50e-06	—-	0.1050131	1.0000000	chr16	87212733
41431	cg02591871	-0.1270	0.0285	8.60e-06	—-	0.1050131	1.0000000	chr19	14228565	PRKACA	TSS200
187357	cg12908187	0.1860	0.0418	8.60e-06	-+++	0.1050131	1.0000000	chr16	88450261
119415	cg07840143	0.1625	0.0372	1.24e-05	++++	0.1438508	1.0000000	chr5	3324860
56100	cg03544320	0.3008	0.0689	1.26e-05	-+++	0.1438508	1.0000000	chr4	5894691	CRMP1	1stExon
330881	cg24053992	0.1754	0.0403	1.38e-05	+-++	0.1468524	1.0000000	chr1	119554564
197997	cg13677022	-0.1546	0.0356	1.39e-05	—-	0.1468524	1.0000000	chr9	34625963	ARID3C	Body
35348	cg02206980	-0.4156	0.0957	1.40e-05	—-	0.1468524	1.0000000	chr6	13574034	SIRT5;SIRT5	TSS1500;TSS1500
240943	cg16734734	0.1558	0.0360	1.52e-05	–++	0.1545099	1.0000000	chr6	105624309	POPDC3;POPDC3	TSS200;5’UTR
64145	cg04080022	-0.1761	0.0409	1.66e-05	—+	0.1646442	1.0000000	chr16	89648534	CPNE7;CPNE7	Body;Body
237459	cg16502049	-0.0984	0.0229	1.71e-05	—-	0.1648080	1.0000000	chr20	23402203	NAPB	TSS200
218644	cg15025362	0.1569	0.0365	1.75e-05	++-+	0.1648080	1.0000000	chr3	186256331	CRYGS	3’UTR
113100	cg07399977	-0.1659	0.0387	1.82e-05	—-	0.1679212	1.0000000	chr1	27339612	FAM46B	TSS1500
301289	cg21629895	-0.1761	0.0412	1.88e-05	—-	0.1679212	1.0000000	chr2	25565795	DNMT3A;DNMT3A;DNMT3A	TSS1500;TSS1500;TSS1500
58832	cg03720762	-0.2458	0.0576	1.96e-05	—-	0.1679212	1.0000000	chr17	17604184	RAI1	5’UTR
168281	cg11414610	-0.1279	0.0300	1.96e-05	—-	0.1679212	1.0000000	chr19	16528319	EPS15L1	Body
176796	cg12065616	-0.1588	0.0373	2.03e-05	—-	0.1700595	1.0000000	chr12	94954828
6030	cg00358880	0.1679	0.0395	2.16e-05	++++	0.1768628	1.0000000	chr1	197885105	LHX9;LHX9	TSS1500;Body
191691	cg13278267	0.1750	0.0414	2.36e-05	++++	0.1847510	1.0000000	chr2	38742843
21418	cg01303372	-0.1905	0.0451	2.43e-05	—-	0.1847510	1.0000000	chr10	121415189	BAG3	Body
228619	cg15830431	0.1587	0.0376	2.43e-05	++-+	0.1847510	1.0000000	chr8	99952591
150668	cg10098010	0.2199	0.0521	2.45e-05	++++	0.1847510	1.0000000	chr6	138483709	KIAA1244	Body
34800	cg02166532	0.1646	0.0392	2.61e-05	++++	0.1883103	1.0000000	chr11	2159853	INS-IGF2;IGF2;IGF2;IGF2;IGF2	Body;Body;5’UTR;5’UTR;1stExon
91398	cg05926253	0.1388	0.0331	2.70e-05	-+++	0.1883103	1.0000000	chr5	1801364	NDUFS6;MRPL36	TSS200;TSS1500
196894	cg13609065	0.0857	0.0204	2.72e-05	-+++	0.1883103	1.0000000	chr17	6613894	SLC13A5;SLC13A5	Body;Body
356139	cg26090406	0.2617	0.0624	2.76e-05	++++	0.1883103	1.0000000	chr13	110937644	COL4A1	Body
50150	cg03149958	-0.1704	0.0408	2.91e-05	—-	0.1883103	1.0000000	chr6	36326677
5363	cg00321074	-0.1267	0.0303	2.92e-05	—-	0.1883103	1.0000000	chr3	19990693	RAB5A	5’UTR
331853	cg24127593	0.1811	0.0433	2.95e-05	++++	0.1883103	1.0000000	chr4	1648399	FAM53A	Body
48278	cg03025061	-0.1653	0.0396	2.96e-05	—-	0.1883103	1.0000000	chr8	109261275	EIF3E	TSS1500
33761	cg02097144	0.1717	0.0411	2.99e-05	+-++	0.1883103	1.0000000	chr7	78280216	MAGI2	Body
117587	cg07712198	0.1970	0.0472	3.04e-05	-+++	0.1883103	1.0000000	chr5	9015582
93	cg00004257	0.2233	0.0536	3.06e-05	++++	0.1883103	1.0000000	chr1	34629175	CSMD2	Body
180441	cg12354986	-0.1980	0.0475	3.09e-05	+—	0.1883103	1.0000000	chr22	38142174	TRIOBP;TRIOBP;TRIOBP	TSS200;Body;TSS200
136896	cg09088406	0.2510	0.0603	3.17e-05	++++	0.1900531	1.0000000	chr15	27819306
323848	cg23504707	0.1527	0.0367	3.24e-05	++++	0.1904752	1.0000000	chr14	60712563	PPM1A;PPM1A	5’UTR;1stExon
80941	cg05197323	-0.1184	0.0285	3.28e-05	+—	0.1904752	1.0000000	chr14	24912098	SDR39U1	TSS200
351351	cg25687423	-0.1619	0.0391	3.47e-05	—-	0.1983951	1.0000000	chr6	43193521	C6orf108;C6orf108	Body;3’UTR
218811	cg15035705	-0.1756	0.0425	3.67e-05	—-	0.2050633	1.0000000	chr5	179159291	MAML1	TSS1500
166619	cg11289100	0.2128	0.0516	3.75e-05	++++	0.2050633	1.0000000	chr17	19313024	RNF112	TSS1500
325843	cg23662713	0.2955	0.0717	3.75e-05	++++	0.2050633	1.0000000	chr14	36741645
217427	cg14931071	0.1339	0.0325	3.80e-05	—+	0.2050633	1.0000000	chr6	12717776	PHACTR1	TSS200
316250	cg22915154	-0.2026	0.0493	3.95e-05	—-	0.2100410	1.0000000	chr11	68816030	TPCN2	TSS1500
247434	cg17260318	-0.1813	0.0442	4.04e-05	—-	0.2118407	1.0000000	chr19	4067604	ZBTB7A	TSS1500
86700	cg05595134	0.3324	0.0811	4.18e-05	+-++	0.2140702	1.0000000	chr8	55047255	MRPL15	TSS1500
292390	cg20899625	-0.1360	0.0332	4.20e-05	—-	0.2140702	1.0000000	chr3	126721131	PLXNA1	Body
352336	cg25763542	-0.2870	0.0702	4.36e-05	—-	0.2160684	1.0000000	chr19	310512	MIER2	Body
20130	cg01218206	-0.1738	0.0426	4.44e-05	—+	0.2160684	1.0000000	chr11	116933977	SIK3	Body
173650	cg11831006	-0.1901	0.0466	4.49e-05	—-	0.2160684	1.0000000	chr3	125100635
307701	cg22193385	-0.1780	0.0436	4.52e-05	–+-	0.2160684	1.0000000	chr12	52638005	KRT7	Body
304218	cg21885638	-0.1256	0.0308	4.53e-05	—-	0.2160684	1.0000000	chr3	129306552	PLXND1	Body
324549	cg23558842	0.2833	0.0695	4.59e-05	++++	0.2160684	1.0000000	chr11	15095178	CALCB;CALCB	1stExon;5’UTR
73455	cg04696969	0.2340	0.0574	4.64e-05	++++	0.2160684	1.0000000	chr2	223335429	SGPP2	Body
233115	cg16188243	-0.2292	0.0564	4.79e-05	—-	0.2192273	1.0000000	chr19	2783719	SGTA	TSS1500
30412	cg01892516	0.4813	0.1184	4.82e-05	++++	0.2192273	1.0000000	chr14	38064532	FOXA1	TSS200
168526	cg11434671	-0.1410	0.0347	4.92e-05	—-	0.2198846	1.0000000	chr17	74524611	CYGB	3’UTR
222274	cg15323873	-0.1523	0.0375	4.95e-05	—-	0.2198846	1.0000000	chr10	79650526	DLG5	Body
168429	cg11425470	-0.1704	0.0420	5.06e-05	—-	0.2221106	1.0000000	chr1	109271795	FNDC7	Body
17916	cg01078824	0.1416	0.0350	5.13e-05	++++	0.2224636	1.0000000	chr7	27220047	HOXA10	TSS200
219413	cg15083775	0.1294	0.0320	5.25e-05	–++	0.2244178	1.0000000	chr17	48054048
228483	cg15822394	-0.1875	0.0464	5.29e-05	—-	0.2244178	1.0000000	chr19	17877733	FCHO1;FCHO1;FCHO1;FCHO1	Body;Body;Body;Body
162133	cg10945313	0.1774	0.0440	5.50e-05	++++	0.2306034	1.0000000	chr4	113739291	ANK2;ANK2	5’UTR;1stExon
223845	cg15454856	0.0991	0.0246	5.76e-05	++-+	0.2389337	1.0000000	chr7	108168130	PNPLA8	TSS1500
225048	cg15557168	0.4852	0.1208	5.90e-05	+-++	0.2414276	1.0000000	chr22	42548783
275492	cg19519624	-0.2199	0.0548	5.96e-05	—-	0.2414276	1.0000000	chr9	138881792
192044	cg13305951	-0.2022	0.0504	6.10e-05	—-	0.2414276	1.0000000	chr17	19314618	RNF112;RNF112	1stExon;5’UTR
330819	cg24049616	0.1591	0.0397	6.22e-05	++++	0.2414276	1.0000000	chr16	55359029	IRX6	1stExon
358903	cg26290114	-0.1633	0.0408	6.22e-05	—-	0.2414276	1.0000000	chr13	52159332	WDFY2	Body
174808	cg11914514	-0.1747	0.0437	6.27e-05	—-	0.2414276	1.0000000	chr9	131218865	ODF2;ODF2	TSS1500;5’UTR
279041	cg19784205	-0.2088	0.0522	6.27e-05	—-	0.2414276	1.0000000	chr12	132473879	EP400	Body
34418	cg02141929	-0.1944	0.0486	6.38e-05	—-	0.2432580	1.0000000	chr16	56681544
134866	cg08928966	0.1305	0.0327	6.58e-05	+-++	0.2459133	1.0000000	chr3	51859710

---

Top 100 GO terms

X	ONTOLOGY	TERM	N	DE	P.DE	FDR
GO:0010800	BP	positive regulation of peptidyl-threonine phosphorylation	28	2	0.0012414	1
GO:0033135	BP	regulation of peptidyl-serine phosphorylation	125	3	0.0014291	1
GO:0030507	MF	spectrin binding	28	2	0.0023516	1
GO:0010494	CC	cytoplasmic stress granule	69	2	0.0031785	1
GO:0010799	BP	regulation of peptidyl-threonine phosphorylation	46	2	0.0034741	1
GO:0005000	MF	vasopressin receptor activity	6	1	0.0035990	1
GO:0032535	BP	regulation of cellular component size	359	4	0.0037773	1
GO:0009258	BP	10-formyltetrahydrofolate catabolic process	2	1	0.0039096	1
GO:0016155	MF	formyltetrahydrofolate dehydrogenase activity	2	1	0.0039096	1
GO:0009397	BP	folic acid-containing compound catabolic process	3	1	0.0042694	1
GO:0042560	BP	pteridine-containing compound catabolic process	3	1	0.0042694	1
GO:0008361	BP	regulation of cell size	169	3	0.0050394	1
GO:0005115	MF	receptor tyrosine kinase-like orphan receptor binding	1	1	0.0052303	1
GO:0036517	BP	chemoattraction of serotonergic neuron axon	1	1	0.0052303	1
GO:0060599	BP	lateral sprouting involved in mammary gland duct morphogenesis	1	1	0.0052303	1
GO:0061347	BP	planar cell polarity pathway involved in outflow tract morphogenesis	1	1	0.0052303	1
GO:0061348	BP	planar cell polarity pathway involved in ventricular septum morphogenesis	1	1	0.0052303	1
GO:0061349	BP	planar cell polarity pathway involved in cardiac right atrium morphogenesis	1	1	0.0052303	1
GO:0061350	BP	planar cell polarity pathway involved in cardiac muscle tissue morphogenesis	1	1	0.0052303	1
GO:0061354	BP	planar cell polarity pathway involved in pericardium morphogenesis	1	1	0.0052303	1
GO:1904934	BP	negative regulation of cell proliferation in midbrain	1	1	0.0052303	1
GO:1904955	BP	planar cell polarity pathway involved in midbrain dopaminergic neuron differentiation	1	1	0.0052303	1
GO:0048850	BP	hypophysis morphogenesis	2	1	0.0056017	1
GO:1905438	BP	non-canonical Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation	2	1	0.0057409	1
GO:0036518	BP	chemorepulsion of dopaminergic neuron axon	2	1	0.0058494	1
GO:0051885	BP	positive regulation of timing of anagen	2	1	0.0058573	1
GO:0097325	BP	melanocyte proliferation	3	1	0.0059866	1
GO:0042695	BP	thelarche	3	1	0.0060342	1
GO:0060744	BP	mammary gland branching involved in thelarche	3	1	0.0060342	1
GO:0060809	BP	mesodermal to mesenchymal transition involved in gastrulation	2	1	0.0060434	1
GO:0060031	BP	mediolateral intercalation	2	1	0.0063463	1
GO:0060775	BP	planar cell polarity pathway involved in gastrula mediolateral intercalation	2	1	0.0063463	1
GO:0060002	MF	plus-end directed microfilament motor activity	3	1	0.0066603	1
GO:1902435	BP	regulation of male mating behavior	2	1	0.0066640	1
GO:1902437	BP	positive regulation of male mating behavior	2	1	0.0066640	1
GO:1904933	BP	regulation of cell proliferation in midbrain	2	1	0.0073534	1
GO:0042640	BP	anagen	5	1	0.0074701	1
GO:0051884	BP	regulation of timing of anagen	5	1	0.0074701	1
GO:0046543	BP	development of secondary female sexual characteristics	5	1	0.0075654	1
GO:0061341	BP	non-canonical Wnt signaling pathway involved in heart development	2	1	0.0077345	1
GO:0061346	BP	planar cell polarity pathway involved in heart morphogenesis	2	1	0.0077345	1
GO:0090081	BP	regulation of heart induction by regulation of canonical Wnt signaling pathway	4	1	0.0077679	1
GO:0090082	BP	positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway	4	1	0.0077679	1
GO:0016742	MF	hydroxymethyl-, formyl- and related transferase activity	8	1	0.0078801	1
GO:0031594	CC	neuromuscular junction	74	2	0.0082890	1
GO:2000243	BP	positive regulation of reproductive process	77	2	0.0083074	1
GO:0045136	BP	development of secondary sexual characteristics	7	1	0.0083250	1
GO:0048022	BP	negative regulation of melanin biosynthetic process	4	1	0.0086266	1
GO:1900377	BP	negative regulation of secondary metabolite biosynthetic process	4	1	0.0086266	1
GO:0090066	BP	regulation of anatomical structure size	491	4	0.0090906	1
GO:0060762	BP	regulation of branching involved in mammary gland duct morphogenesis	4	1	0.0091396	1
GO:0060067	BP	cervix development	2	1	0.0093337	1
GO:0003308	BP	negative regulation of Wnt signaling pathway involved in heart development	7	1	0.0094248	1
GO:0003408	BP	optic cup formation involved in camera-type eye development	3	1	0.0098302	1
GO:0003138	BP	primary heart field specification	3	1	0.0099138	1
GO:0060157	BP	urinary bladder development	4	1	0.0101397	1
GO:0009256	BP	10-formyltetrahydrofolate metabolic process	5	1	0.0101432	1
GO:1902379	MF	chemoattractant activity involved in axon guidance	2	1	0.0101929	1
GO:0021953	BP	central nervous system neuron differentiation	186	3	0.0102959	1
GO:0001025	MF	RNA polymerase III general transcription initiation factor binding	3	1	0.0103155	1
GO:0001156	MF	TFIIIC-class transcription factor complex binding	3	1	0.0103155	1
GO:0048818	BP	positive regulation of hair follicle maturation	5	1	0.0103953	1
GO:0001002	MF	RNA polymerase III type 1 promoter sequence-specific DNA binding	3	1	0.0103974	1
GO:0001003	MF	RNA polymerase III type 2 promoter sequence-specific DNA binding	3	1	0.0103974	1
GO:0080084	MF	5S rDNA binding	3	1	0.0103974	1
GO:0003213	BP	cardiac right atrium morphogenesis	2	1	0.0106682	1
GO:0048852	BP	diencephalon morphogenesis	3	1	0.0108245	1
GO:0106006	MF	cytoskeletal protein-membrane anchor activity	3	1	0.0109384	1
GO:0060750	BP	epithelial cell proliferation involved in mammary gland duct elongation	3	1	0.0110411	1
GO:0060751	BP	branch elongation involved in mammary gland duct branching	3	1	0.0110411	1
GO:0038031	BP	non-canonical Wnt signaling pathway via JNK cascade	6	1	0.0113371	1
GO:0098732	BP	macromolecule deacylation	101	2	0.0116357	1
GO:0070245	BP	positive regulation of thymocyte apoptotic process	5	1	0.0118200	1
GO:0034983	BP	peptidyl-lysine deacetylation	7	1	0.0118657	1
GO:0001938	BP	positive regulation of endothelial cell proliferation	107	2	0.0118838	1
GO:0033138	BP	positive regulation of peptidyl-serine phosphorylation	91	2	0.0120043	1
GO:0100012	BP	regulation of heart induction by canonical Wnt signaling pathway	5	1	0.0121810	1
GO:0060029	BP	convergent extension involved in organogenesis	6	1	0.0122571	1
GO:0061702	CC	inflammasome complex	15	1	0.0127027	1
GO:0036515	BP	serotonergic neuron axon guidance	4	1	0.0128115	1
GO:0097476	BP	spinal cord motor neuron migration	4	1	0.0129507	1
GO:0015386	MF	potassium:proton antiporter activity	9	1	0.0131411	1
GO:0045927	BP	positive regulation of growth	250	3	0.0132418	1
GO:0036514	BP	dopaminergic neuron axon guidance	5	1	0.0134260	1
GO:1904938	BP	planar cell polarity pathway involved in axon guidance	5	1	0.0134260	1
GO:0018105	BP	peptidyl-serine phosphorylation	282	3	0.0134792	1
GO:0015385	MF	sodium:proton antiporter activity	10	1	0.0135356	1
GO:1901216	BP	positive regulation of neuron death	91	2	0.0139154	1
GO:0071374	BP	cellular response to parathyroid hormone stimulus	8	1	0.0139668	1
GO:0071233	BP	cellular response to leucine	10	1	0.0141602	1
GO:0060340	BP	positive regulation of type I interferon-mediated signaling pathway	13	1	0.0142616	1
GO:0038030	BP	non-canonical Wnt signaling pathway via MAPK cascade	7	1	0.0143467	1
GO:0003307	BP	regulation of Wnt signaling pathway involved in heart development	9	1	0.0144283	1
GO:0060090	MF	molecular adaptor activity	302	3	0.0144754	1
GO:0002862	BP	negative regulation of inflammatory response to antigenic stimulus	14	1	0.0148018	1
GO:0044851	BP	hair cycle phase	9	1	0.0149027	1
GO:0048819	BP	regulation of hair follicle maturation	9	1	0.0149027	1
GO:0005451	MF	monovalent cation:proton antiporter activity	11	1	0.0152620	1
GO:0021954	BP	central nervous system neuron development	78	2	0.0153361	1
GO:0071107	BP	response to parathyroid hormone	10	1	0.0155003	1

---

DVPs

DVP datasets for common CpGs

# results adjusted for age, sex, smoking

fact850_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMC_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DVPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)
chileBuccal_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DVPs_updated-results_2020-11-29/age-sex-smoking.txt', sep = "\t", header = T)

fact850_DVP = fact850_DVP[fact850_DVP$cpg %in% allCpg,]
fact450_DVP = fact450_DVP[fact450_DVP$cpg %in% allCpg,]
chilePBMC_DVP = chilePBMC_DVP[chilePBMC_DVP$cpg %in% allCpg,]
chileBuccal_DVP = chileBuccal_DVP[chileBuccal_DVP$cpg %in% allCpg,]

write.table(fact850_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMC_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccal_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)


# results adjusted for age, sex, smoking, cells

fact850cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_092520.txt', sep = "\t", header = T)
fact450cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_092520.txt', sep = "\t", header = T)
chilePBMCcell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_PBMCs_DVPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)
chileBuccalcell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/Chile_buccal_DVPs_updated-results_2020-11-29/cell-age-sex-smoking.txt', sep = "\t", header = T)

fact850cell_DVP = fact850cell_DVP[fact850cell_DVP$cpg %in% allCpg,]
fact450cell_DVP = fact450cell_DVP[fact450cell_DVP$cpg %in% allCpg,]
chilePBMCcell_DVP = chilePBMCcell_DVP[chilePBMCcell_DVP$cpg %in% allCpg,]
chileBuccalcell_DVP = chileBuccalcell_DVP[chileBuccalcell_DVP$cpg %in% allCpg,]

write.table(fact850cell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(fact450cell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chilePBMCcell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)
write.table(chileBuccalcell_DVP, file = "/Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_DVP_120420_common.txt", sep = "\t", row.names = FALSE, col.names = TRUE)

Run in METAL

cd /Users/annebozack/Documents/arsenic_meta/generic-metal

MARKER "cpg"
EFFECT "DiffLevene"
PVAL "P.Value"
STDERR "std_err"
SCHEME STDERR

# SCHEME STDERR command and weights effect size estimates using the inverse of the corresponding standard errors
    
# no cell type adjustment, blood only
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_DVP_120420 .tbl

ANALYZE

# no cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-age-sex-smoking_DVP_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_DVP_120420 .tbl

ANALYZE

# cell type adjustment, blood only  
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_DVP_120420 .tbl

ANALYZE

# cell type adjustment, all samples
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_850k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/FACT_DVP_AsCategorical_adjCellAgeSm_450k_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-pbmcs-cell-age-sex-smoking_DVP_120420_common.txt
PROCESS /Users/annebozack/Documents/arsenic_meta/generic-metal/chile-buccal-cell-age-sex-smoking_DVP_120420_common.txt
OUTFILE /Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_DVP_120420 .tbl

ANALYZE

Without cell type adjustment

Blood only

metal_blood_noCell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_no_cell_common_DVP_1204201.tbl', sep = "\t")

metal_blood_noCell_DVP = metalProcess(metal_blood_noCell_DVP)

write.csv(metal_blood_noCell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_blood_no_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_blood_noCell_DVP$P.value < 0.05)
#  FALSE   TRUE 
# 350920  26431

# FDR
table(metal_blood_noCell_DVP$P.FDR < 0.05)
# FALSE   TRUE 
# 377326     25 

table(metal_blood_noCell_DVP$P.FDR < 0.1)
# FALSE   TRUE 
# 377306     45 

# Bonferroni
table(metal_blood_noCell_DVP$P.Bonf < 0.05)
# FALSE   TRUE 
# 377346     5 


# GO analysis, FDR < 0.1 probes

go_metal_blood_noCell_DVP = gometh(sig.cpg = metal_blood_noCell_DVP$Name[metal_blood_noCell_DVP$P.FDR < 0.1], all.cpg = metal_blood_noCell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_blood_noCell_DVP = go_metal_blood_noCell_DVP[order(go_metal_blood_noCell_DVP$P.DE),]

table(go_metal_blood_noCell_DVP$P.DE<0.05)
# FALSE  TRUE 
# 22453   130 

table(go_metal_blood_noCell_DVP$FDR<0.05)
# FALSE  
# 22583 

write.csv(go_metal_blood_noCell_DVP[go_metal_blood_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_blood_noCell_common_120420.csv')


# KEGG analysis, FDR < 0.1 probes

kegg_metal_blood_noCell_DVP = gometh(sig.cpg = metal_blood_noCell_DVP$Name[metal_blood_noCell_DVP$P.FDR < 0.1], all.cpg = metal_blood_noCell_DVP$Name, array.type = '450K', collection = 'KEGG', anno = annAll2)
kegg_metal_blood_noCell_DVP = kegg_metal_blood_noCell_DVP[order(kegg_metal_blood_noCell_DVP$P.DE),]

table(kegg_metal_blood_noCell_DVP$P.DE<0.05)
# FALSE  TRUE 
#  335     5 

table(kegg_metal_blood_noCell_DVP$FDR<0.05)
# FALSE  
# 340

write.csv(kegg_metal_blood_noCell_DVP[kegg_metal_blood_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_blood_noCell_common_120420.csv')


# Plotting

gg_qqplot(metal_blood_noCell_DVP$P.value)
quartz.save('qq_metal_blood_noCell_DVP_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_blood_noCell_DVP, FDR=T)
quartz.save('manhattan_metal_blood_noCell_DVP_120420.png', type = "png", dpi = 300)

volcano_meta(metal_blood_noCell_DVP, FDR = TRUE)
quartz.save('volcano_metal_blood_noCell_DVP_120420.png', type = "png", dpi = 300)

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_noCell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_noCell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_noCell_DVP_120420.png")

Top 100 probes

X	Name	Effect	StdErr	P.value	Direction	P.FDR	P.Bonf	chr	pos	UCSC_RefGene_Name	UCSC_RefGene_Group
321132	cg23281729	0.9488	0.1212	0.00e+00	-++	0.0000000	0.0000000	chr18	78005477	PARD6G	TSS200
268961	cg18971529	0.3420	0.0614	0.00e+00	++-	0.0037974	0.0094036	chr21	30391563	RWDD2B	1stExon
50934	cg03205258	0.5963	0.1076	0.00e+00	+++	0.0037974	0.0113922	chr22	19929274	TXNRD2;COMT;COMT	1stExon;1stExon;5’UTR
10618	cg00629117	0.9092	0.1674	1.00e-07	+++	0.0052395	0.0209581	chr16	1844932	IGFALS;IGFALS;IGFALS	TSS200;TSS1500;TSS1500
309909	cg22387890	0.5327	0.0993	1.00e-07	+++	0.0060852	0.0304258	chr7	6145595	USP42	5’UTR
163279	cg11032634	0.6573	0.1251	1.00e-07	+++	0.0092765	0.0556593	chr22	19929254	TXNRD2;COMT	1stExon;TSS200
189046	cg13054212	0.1060	0.0204	2.00e-07	+++	0.0095797	0.0791305	chr4	186356202	C4orf47	Body
282819	cg20074307	0.0884	0.0171	2.00e-07	+++	0.0095797	0.0892812	chr14	55092491	SAMD4A;SAMD4A	Body;Body
261543	cg18380742	0.1049	0.0203	2.00e-07	+++	0.0095797	0.0915831	chr1	61674366	NFIA;NFIA;NFIA;NFIA	Body;Body;Body;Body
32578	cg02026246	0.1680	0.0328	3.00e-07	+++	0.0095797	0.1129412	chr11	22687589	GAS2	TSS1500
374163	cg27425262	0.7281	0.1422	3.00e-07	+++	0.0095797	0.1152807	chr2	113953981	PSD4;LOC440839	Body;Body
145256	cg09692492	-0.3016	0.0590	3.00e-07	—	0.0095797	0.1192052	chr22	23744717	ZDHHC8P	Body
199880	cg13797228	0.1148	0.0225	3.00e-07	+++	0.0095797	0.1270541	chr3	126076243	KLF15	TSS200
237588	cg16511076	0.1132	0.0223	4.00e-07	+++	0.0095797	0.1435821	chr4	48887480	OCIAD2;OCIAD2	3’UTR;3’UTR
171628	cg11691429	0.1834	0.0361	4.00e-07	+++	0.0095797	0.1436953	chr2	947634	SNTG2	Body
149284	cg09996597	0.4748	0.0945	5.00e-07	+++	0.0118134	0.1890151	chr16	1844927	IGFALS;IGFALS;IGFALS	TSS200;TSS1500;TSS1500
2783	cg00156336	-0.1921	0.0384	5.00e-07	—	0.0121840	0.2071280	chr2	75788423	FAM176A;FAM176A	5’UTR;TSS1500
124685	cg08207566	0.1099	0.0224	1.00e-06	+++	0.0205510	0.3699172	chr4	174086461
93087	cg06039392	0.1376	0.0282	1.00e-06	+++	0.0205954	0.3913130	chr4	187476953	MTNR1A	TSS1500
41466	cg02593924	0.2792	0.0583	1.70e-06	+++	0.0318107	0.6362138	chr16	1844998	IGFALS;IGFALS;IGFALS	TSS200;TSS1500;TSS1500
313664	cg22712983	-0.2209	0.0464	1.90e-06	–+	0.0332583	0.7139481	chr2	219187374	PNKD;PNKD	TSS1500;Body
325001	cg23602489	0.1012	0.0213	1.90e-06	+++	0.0332583	0.7316836	chr7	101508949	CUX1;CUX1;CUX1	Body;Body;Body
121859	cg08015590	-0.4238	0.0896	2.30e-06	—	0.0372265	0.8562094	chr7	2281924	NUDT1;NUDT1;NUDT1;NUDT1;NUDT1;NUDT1;FTSJ2;NUDT1;NUDT1;NUDT1	5’UTR;5’UTR;1stExon;TSS1500;5’UTR;5’UTR;TSS200;1stExon;5’UTR;TSS1500
135062	cg08942080	0.1515	0.0321	2.40e-06	+++	0.0383483	0.9203591	chr12	124821568	NCOR2;NCOR2	Body;Body
169144	cg11494866	0.1017	0.0218	3.10e-06	+++	0.0463085	1.0000000	chr8	42695070	THAP1;THAP1	Body;Body
516	cg00026731	-0.1223	0.0264	3.60e-06	—	0.0521470	1.0000000	chr18	55254092	FECH;FECH	TSS200;TSS200
190991	cg13221086	0.1023	0.0223	4.30e-06	+++	0.0595935	1.0000000	chr3	31809318	OSBPL10	Body
293675	cg21004290	0.1140	0.0249	4.50e-06	+++	0.0611578	1.0000000	chr8	131250320	ASAP1	Body
301219	cg21623748	0.0943	0.0206	4.80e-06	+++	0.0625101	1.0000000	chr12	54378787	HOXC10	TSS200
9019	cg00534624	0.2751	0.0604	5.20e-06	+++	0.0632577	1.0000000	chr16	1845096	IGFALS;IGFALS;IGFALS	TSS200;TSS1500;TSS1500
194801	cg13483984	0.1164	0.0256	5.50e-06	+++	0.0632577	1.0000000	chr1	224580455	WDR26;WDR26	Body;Body
268251	cg18907098	0.0733	0.0161	5.50e-06	+++	0.0632577	1.0000000	chr4	512994	PIGG;PIGG	Body;Body
168599	cg11440940	0.0987	0.0217	5.50e-06	+++	0.0632577	1.0000000	chr19	8510764	HNRNPM;HNRNPM	Body;Body
259345	cg18206914	0.0839	0.0185	5.80e-06	+++	0.0640024	1.0000000	chr22	50963825	SCO2;SCO2;SCO2;SCO2	5’UTR;5’UTR;5’UTR;5’UTR
156274	cg10502904	0.1611	0.0356	6.10e-06	+++	0.0640024	1.0000000	chr10	131565289	MGMT	3’UTR
132616	cg08770961	0.2938	0.0651	6.30e-06	+++	0.0640024	1.0000000	chr16	66956122	RRAD;RRAD	Body;Body
59640	cg03770962	0.1059	0.0235	6.40e-06	+++	0.0640024	1.0000000	chr7	148477754	CUL1	Body
64658	cg04111999	0.0991	0.0220	6.50e-06	+++	0.0640024	1.0000000	chr10	22615540	BMI1	Body
335850	cg24454243	-0.2036	0.0452	6.70e-06	—	0.0640024	1.0000000	chr7	105221985	EFCAB10	TSS200
229928	cg15931233	0.0956	0.0212	6.80e-06	+++	0.0640024	1.0000000	chr5	53455496	ARL15	Body
80568	cg05169951	0.1850	0.0411	7.00e-06	+++	0.0640024	1.0000000	chr16	3017955	KREMEN2;PAQR4;KREMEN2	Body;TSS1500;Body
178342	cg12175949	0.3443	0.0769	7.60e-06	+++	0.0679591	1.0000000	chr22	19929286	TXNRD2;COMT;COMT	1stExon;1stExon;5’UTR
259615	cg18228116	0.3258	0.0735	9.30e-06	-++	0.0820168	1.0000000	chr10	133995345	JAKMIP3	3’UTR
349119	cg25499746	0.0792	0.0179	9.90e-06	+++	0.0845695	1.0000000	chr6	16346054	ATXN1;ATXN1	5’UTR;5’UTR
48009	cg03004999	-0.0816	0.0186	1.15e-05	—	0.0960149	1.0000000	chr7	43152125	HECW1	TSS200
26185	cg01614020	0.2522	0.0577	1.24e-05	+++	0.1014746	1.0000000	chr8	24814137	NEFL	TSS200
240531	cg16707423	0.0797	0.0183	1.29e-05	+++	0.1016671	1.0000000	chr1	227167020	CABC1	Body
38724	cg02415779	0.1130	0.0259	1.32e-05	-++	0.1016671	1.0000000	chr22	18527778
323330	cg23463533	0.0930	0.0214	1.33e-05	+++	0.1016671	1.0000000	chr7	154473289	DPP6;DPP6;DPP6	Body;Body;Body
129911	cg08575722	-0.1195	0.0275	1.36e-05	—	0.1016671	1.0000000	chr11	32421845	WT1;WT1;WT1;WT1	Body;Body;Body;Body
70352	cg04485956	0.2005	0.0461	1.38e-05	+++	0.1016671	1.0000000	chr2	1859071	MYT1L	Body
80361	cg05157266	0.1358	0.0313	1.40e-05	+++	0.1016671	1.0000000	chr2	183901614	NCKAP1;NCKAP1	Body;Body
320947	cg23268677	0.2705	0.0625	1.50e-05	+++	0.1051691	1.0000000	chr22	19929097	TXNRD2;COMT	Body;TSS200
353609	cg25880954	0.7380	0.1705	1.50e-05	+++	0.1051691	1.0000000	chr1	47900630	MGC12982;FOXD2	TSS1500;TSS1500
297153	cg21270743	0.0928	0.0215	1.61e-05	+++	0.1061227	1.0000000	chr1	156475001
191701	cg13279009	0.0804	0.0187	1.63e-05	-++	0.1061227	1.0000000	chr2	24584023	ITSN2;ITSN2;ITSN2	TSS1500;TSS1500;TSS1500
305009	cg21951425	-0.1330	0.0309	1.63e-05	—	0.1061227	1.0000000	chr15	26108612	ATP10A	TSS1500
291461	cg20805880	0.1028	0.0239	1.68e-05	+++	0.1061227	1.0000000	chr15	73367293	NEO1	Body
332989	cg24215973	0.2223	0.0517	1.73e-05	+++	0.1061227	1.0000000	chr2	240111563	HDAC4	Body
282764	cg20070659	0.2554	0.0595	1.76e-05	-++	0.1061227	1.0000000	chr4	188736336
25526	cg01570086	-0.1220	0.0284	1.77e-05	—	0.1061227	1.0000000	chr15	74833080	ARID3B	TSS1500
176205	cg12024822	0.1823	0.0425	1.81e-05	+++	0.1061227	1.0000000	chr6	90597394
193732	cg13423098	0.1394	0.0325	1.81e-05	+++	0.1061227	1.0000000	chr15	23807234
11224	cg00668103	0.1128	0.0263	1.82e-05	+++	0.1061227	1.0000000	chr7	100084730	C7orf51	Body
196530	cg13587236	0.0904	0.0211	1.83e-05	+++	0.1061227	1.0000000	chr9	128472496
361112	cg26453295	0.0812	0.0190	1.94e-05	+++	0.1093224	1.0000000	chr19	54851740	LILRA4	TSS1500
329980	cg23990236	0.1245	0.0292	1.96e-05	-++	0.1093224	1.0000000	chr1	12220146
223604	cg15439717	0.1095	0.0257	1.98e-05	+++	0.1093224	1.0000000	chr13	23993016	SACS	5’UTR
309271	cg22336633	-0.1142	0.0268	2.00e-05	—	0.1093224	1.0000000	chr11	17099688	RPS13	TSS1500
127440	cg08400962	0.1029	0.0242	2.04e-05	+++	0.1094849	1.0000000	chr19	34112316	CHST8;CHST8	TSS1500;TSS1500
299250	cg21476203	0.1083	0.0254	2.06e-05	+++	0.1094849	1.0000000	chr8	144874281	SCRIB;SCRIB	Body;Body
39898	cg02492873	0.1056	0.0248	2.14e-05	++-	0.1111146	1.0000000	chr2	25193821	DNAJC27	Body
110491	cg07219314	-0.1568	0.0369	2.17e-05	—	0.1111146	1.0000000	chr22	23744725	ZDHHC8P	Body
153889	cg10322744	0.4290	0.1011	2.18e-05	+++	0.1111146	1.0000000	chr12	98910138	TMPO;TMPO;TMPO;LOC100128191	Body;Body;Body;TSS200
203197	cg14002714	0.1309	0.0310	2.37e-05	-++	0.1192429	1.0000000	chr14	56095810	KTN1;KTN1;KTN1;KTN1	Body;Body;Body;Body
110227	cg07202461	0.0845	0.0201	2.53e-05	+++	0.1257671	1.0000000	chr18	19406765	MIB1;MIR133A1	Body;TSS1500
50532	cg03176729	0.3304	0.0785	2.59e-05	+++	0.1269762	1.0000000	chr10	124222607	HTRA1	Body
193559	cg13411311	-0.0913	0.0217	2.66e-05	—	0.1277739	1.0000000	chr2	241095989
157333	cg10577216	-0.1585	0.0377	2.68e-05	—	0.1277739	1.0000000	chr6	143265045	HIVEP2	5’UTR
111485	cg07290190	0.0927	0.0221	2.85e-05	++-	0.1313439	1.0000000	chr4	121992756	C4orf31	5’UTR
59636	cg03770787	-0.2358	0.0564	2.87e-05	—	0.1313439	1.0000000	chr15	65652019	IGDCC3	Body
96749	cg06319359	0.0756	0.0181	2.88e-05	+++	0.1313439	1.0000000	chr1	22109595	USP48;USP48;USP48;USP48	5’UTR;5’UTR;1stExon;1stExon
364539	cg26706070	0.0913	0.0218	2.89e-05	+++	0.1313439	1.0000000	chr16	31119936	BCKDK;BCKDK	5’UTR;5’UTR
185794	cg12778178	0.1033	0.0247	2.93e-05	+++	0.1313439	1.0000000	chr20	62583555	UCKL1AS;UCKL1	TSS1500;Body
147224	cg09845489	0.2355	0.0564	3.00e-05	+++	0.1313439	1.0000000	chr7	157667853	PTPRN2;PTPRN2;PTPRN2	Body;Body;Body
259108	cg18190030	-0.1190	0.0285	3.03e-05	+–	0.1313439	1.0000000	chr1	234348636	SLC35F3	Body
58766	cg03717570	0.1286	0.0308	3.04e-05	+++	0.1313439	1.0000000	chr17	73316496	GRB2;GRB2	Body;Body
155786	cg10468535	0.1263	0.0303	3.06e-05	+++	0.1313439	1.0000000	chr7	157792053	PTPRN2;PTPRN2;PTPRN2	Body;Body;Body
125889	cg08285768	0.0863	0.0208	3.29e-05	+++	0.1354434	1.0000000	chr15	86038622	AKAP13;AKAP13	Body;Body
116632	cg07642445	0.0668	0.0161	3.30e-05	+++	0.1354434	1.0000000	chr6	27855795
261990	cg18414754	0.1826	0.0440	3.32e-05	+++	0.1354434	1.0000000	chr3	138668832	C3orf72	Body
235393	cg16353272	0.0827	0.0199	3.34e-05	+++	0.1354434	1.0000000	chr16	2124240	TSC2;TSC2;TSC2	Body;Body;Body
295936	cg21185289	0.2892	0.0698	3.38e-05	+++	0.1354434	1.0000000	chr2	74743437	TLX2	3’UTR
351214	cg25674826	0.2435	0.0587	3.38e-05	+++	0.1354434	1.0000000	chr21	35446543	MRPS6;SLC5A3	Body;5’UTR
253963	cg17805202	0.1087	0.0262	3.45e-05	+++	0.1354434	1.0000000	chr1	239937440	CHRM3	5’UTR
90239	cg05850971	0.0924	0.0223	3.53e-05	+++	0.1354434	1.0000000	chr6	32135027	EGFL8	Body
12204	cg00729699	-0.0914	0.0221	3.58e-05	—	0.1354434	1.0000000	chr8	21918075	EPB49;EPB49;EPB49;EPB49;EPB49;EPB49	5’UTR;5’UTR;5’UTR;5’UTR;5’UTR;5’UTR
363304	cg26618618	0.0956	0.0231	3.58e-05	+++	0.1354434	1.0000000	chr11	95661178
355638	cg26051433	0.0958	0.0232	3.61e-05	+++	0.1354434	1.0000000	chr10	75001410	FAM149B1	3’UTR
11047	cg00657529	0.0832	0.0201	3.61e-05	+++	0.1354434	1.0000000	chr6	31698687	CLIC1;DDAH2	Body;TSS1500

---

Top 100 GO terms

X	ONTOLOGY	TERM	N	DE	P.DE	FDR
GO:0004325	MF	ferrochelatase activity	1	1	0.0015112	1
GO:0042053	BP	regulation of dopamine metabolic process	17	2	0.0018929	1
GO:0042069	BP	regulation of catecholamine metabolic process	17	2	0.0018929	1
GO:0015036	MF	disulfide oxidoreductase activity	39	2	0.0027763	1
GO:0070541	BP	response to platinum ion	3	1	0.0039000	1
GO:0016363	CC	nuclear matrix	103	3	0.0039500	1
GO:2000815	BP	regulation of mRNA stability involved in response to oxidative stress	2	1	0.0041977	1
GO:0031337	BP	positive regulation of sulfur amino acid metabolic process	1	1	0.0061113	1
GO:0050668	BP	positive regulation of homocysteine metabolic process	1	1	0.0061113	1
GO:0042417	BP	dopamine metabolic process	33	2	0.0061305	1
GO:0016667	MF	oxidoreductase activity, acting on a sulfur group of donors	57	2	0.0063848	1
GO:0034399	CC	nuclear periphery	124	3	0.0065066	1
GO:0051267	MF	CP2 mannose-ethanolamine phosphotransferase activity	1	1	0.0065613	1
GO:0003908	MF	methylated-DNA-[protein]-cysteine S-methyltransferase activity	1	1	0.0074068	1
GO:0050666	BP	regulation of homocysteine metabolic process	2	1	0.0075457	1
GO:0001544	BP	initiation of primordial ovarian follicle growth	2	1	0.0083648	1
GO:0000301	BP	retrograde transport, vesicle recycling within Golgi	2	1	0.0085027	1
GO:0004416	MF	hydroxyacylglutathione hydrolase activity	2	1	0.0087442	1
GO:0019243	BP	methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione	2	1	0.0087442	1
GO:0051377	MF	mannose-ethanolamine phosphotransferase activity	4	1	0.0090417	1
GO:0008502	MF	melatonin receptor activity	3	1	0.0090824	1
GO:0045764	BP	positive regulation of cellular amino acid metabolic process	3	1	0.0091048	1
GO:0016206	MF	catechol O-methyltransferase activity	2	1	0.0092874	1
GO:0102084	MF	L-dopa O-methyltransferase activity	2	1	0.0092874	1
GO:0102938	MF	orcinol O-methyltransferase activity	2	1	0.0092874	1
GO:0006584	BP	catecholamine metabolic process	46	2	0.0094643	1
GO:0009712	BP	catechol-containing compound metabolic process	46	2	0.0094643	1
GO:0016036	BP	cellular response to phosphate starvation	2	1	0.0096037	1
GO:0031335	BP	regulation of sulfur amino acid metabolic process	3	1	0.0096910	1
GO:0051596	BP	methylglyoxal catabolic process	3	1	0.0106621	1
GO:0061727	BP	methylglyoxal catabolic process to lactate	3	1	0.0106621	1
GO:0005759	CC	mitochondrial matrix	452	4	0.0107974	1
GO:0010610	BP	regulation of mRNA stability involved in response to stress	3	1	0.0109776	1
GO:0035814	BP	negative regulation of renal sodium excretion	3	1	0.0110177	1
GO:0001786	MF	phosphatidylserine binding	56	2	0.0116723	1
GO:1901842	BP	negative regulation of high voltage-gated calcium channel activity	4	1	0.0119888	1
GO:0042382	CC	paraspeckles	6	1	0.0126671	1
GO:0051176	BP	positive regulation of sulfur metabolic process	3	1	0.0130321	1
GO:0042698	BP	ovulation cycle	69	2	0.0133490	1
GO:0009438	BP	methylglyoxal metabolic process	5	1	0.0142031	1
GO:0008172	MF	S-methyltransferase activity	6	1	0.0142529	1
GO:0006513	BP	protein monoubiquitination	66	2	0.0142928	1
GO:0045914	BP	negative regulation of catecholamine metabolic process	3	1	0.0143262	1
GO:0045963	BP	negative regulation of dopamine metabolic process	3	1	0.0143262	1
GO:0016013	CC	syntrophin complex	3	1	0.0147056	1
GO:0033238	BP	regulation of cellular amine metabolic process	78	2	0.0147491	1
GO:0046501	BP	protoporphyrinogen IX metabolic process	10	1	0.0156773	1
GO:0042420	BP	dopamine catabolic process	5	1	0.0160319	1
GO:1903527	BP	positive regulation of membrane tubulation	4	1	0.0162069	1
GO:1990452	CC	Parkin-FBXW7-Cul1 ubiquitin ligase complex	3	1	0.0162837	1
GO:0050773	BP	regulation of dendrite development	141	3	0.0170721	1
GO:0042180	BP	cellular ketone metabolic process	251	3	0.0178267	1
GO:0032413	BP	negative regulation of ion transmembrane transporter activity	72	2	0.0182638	1
GO:0051597	BP	response to methylmercury	7	1	0.0188400	1
GO:0071535	MF	RING-like zinc finger domain binding	4	1	0.0190520	1
GO:0019614	BP	catechol-containing compound catabolic process	6	1	0.0191770	1
GO:0042424	BP	catecholamine catabolic process	6	1	0.0191770	1
GO:0042567	CC	insulin-like growth factor ternary complex	4	1	0.0192472	1
GO:0042182	BP	ketone catabolic process	12	1	0.0199094	1
GO:0016942	CC	insulin-like growth factor binding protein complex	5	1	0.0201819	1
GO:0036454	CC	growth factor complex	5	1	0.0201819	1
GO:0046916	BP	cellular transition metal ion homeostasis	104	2	0.0202261	1
GO:0072341	MF	modified amino acid binding	84	2	0.0204407	1
GO:0004791	MF	thioredoxin-disulfide reductase activity	7	1	0.0208452	1
GO:0001547	BP	antral ovarian follicle growth	8	1	0.0217342	1
GO:1903525	BP	regulation of membrane tubulation	6	1	0.0219949	1
GO:0036353	BP	histone H2A-K119 monoubiquitination	8	1	0.0220516	1
GO:0034046	MF	poly(G) binding	7	1	0.0226594	1
GO:0009008	MF	DNA-methyltransferase activity	6	1	0.0227584	1
GO:0006878	BP	cellular copper ion homeostasis	12	1	0.0230298	1
GO:0032410	BP	negative regulation of transporter activity	83	2	0.0231043	1
GO:0010265	BP	SCF complex assembly	6	1	0.0236882	1
GO:0033239	BP	negative regulation of cellular amine metabolic process	6	1	0.0243470	1
GO:0042405	CC	nuclear inclusion body	12	1	0.0243529	1
GO:0046185	BP	aldehyde catabolic process	12	1	0.0244393	1
GO:0016668	MF	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor	11	1	0.0250461	1
GO:0033240	BP	positive regulation of cellular amine metabolic process	7	1	0.0250550	1
GO:1904063	BP	negative regulation of cation transmembrane transport	86	2	0.0250751	1
GO:0019336	BP	phenol-containing compound catabolic process	9	1	0.0258713	1
GO:0000151	CC	ubiquitin ligase complex	273	3	0.0259841	1
GO:0055070	BP	copper ion homeostasis	14	1	0.0260912	1
GO:0051051	BP	negative regulation of transport	456	4	0.0264663	1
GO:0007614	BP	short-term memory	10	1	0.0266638	1
GO:0044106	BP	cellular amine metabolic process	122	2	0.0269691	1
GO:0006825	BP	copper ion transport	15	1	0.0270306	1
GO:0042135	BP	neurotransmitter catabolic process	9	1	0.0279874	1
GO:0006307	BP	DNA dealkylation involved in DNA repair	10	1	0.0282932	1
GO:0051537	MF	2 iron, 2 sulfur cluster binding	21	1	0.0287087	1
GO:0009308	BP	amine metabolic process	131	2	0.0295977	1
GO:0071803	BP	positive regulation of podosome assembly	10	1	0.0296441	1
GO:0042762	BP	regulation of sulfur metabolic process	13	1	0.0299326	1
GO:0050667	BP	homocysteine metabolic process	13	1	0.0314888	1
GO:0071014	CC	post-mRNA release spliceosomal complex	13	1	0.0323889	1
GO:0033617	BP	mitochondrial cytochrome c oxidase assembly	21	1	0.0324808	1
GO:0048609	BP	multicellular organismal reproductive process	769	5	0.0325911	1
GO:0015035	MF	protein disulfide oxidoreductase activity	21	1	0.0331027	1
GO:0016254	BP	preassembly of GPI anchor in ER membrane	16	1	0.0331426	1
GO:0017085	BP	response to insecticide	11	1	0.0333218	1
GO:0046929	BP	negative regulation of neurotransmitter secretion	10	1	0.0333587	1
GO:0034766	BP	negative regulation of ion transmembrane transport	97	2	0.0333662	1

Including buccal

metal_all_noCell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_no_cell_common_DVP_1204201.tbl', sep = "\t")

metal_all_noCell_DVP = metalProcess(metal_all_noCell_DVP)

write.csv(metal_all_noCell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_all_no_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_all_noCell_DVP$P.value < 0.05)
#  FALSE   TRUE 
# 352439  24912

# FDR
table(metal_all_noCell_DVP$P.FDR < 0.05)
# FALSE     TRUE
# 377331     20 

table(metal_all_noCell_DVP$P.FDR < 0.1)
# FALSE     TRUE
# 377310     41  

# Bonferroni
table(metal_all_noCell_DVP$P.Bonf < 0.05)
# FALSE     TRUE
# 377346      5  


# GO analysis, FDR < 0.1 probes

go_metal_all_noCell_DVP = gometh(sig.cpg = metal_all_noCell_DVP$Name[metal_all_noCell_DVP$P.FDR < 0.1], all.cpg = metal_all_noCell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_all_noCell_DVP = go_metal_all_noCell_DVP[order(go_metal_all_noCell_DVP$P.DE),]

table(go_metal_all_noCell_DVP$P.DE<0.05)
# FALSE  TRUE 
#  22387   196 

table(go_metal_all_noCell_DVP$FDR<0.05)
# FALSE 
# 22583 

write.csv(go_metal_all_noCell_DVP[go_metal_all_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_all_noCell_common_120420.csv')


# KEGG analysis, FDR < 0.1 probes

kegg_metal_all_noCell_DVP = gometh(sig.cpg = metal_all_noCell_DVP$Name[metal_all_noCell_DVP$P.FDR < 0.1], all.cpg = metal_all_noCell_DVP$Name, array.type = '450K', collection = 'KEGG', anno = annAll2)
kegg_metal_all_noCell_DVP = kegg_metal_all_noCell_DVP[order(kegg_metal_all_noCell_DVP$P.DE),]

table(kegg_metal_all_noCell_DVP$P.DE<0.05)
# FALSE  TRUE 
#  336     4  

table(kegg_metal_all_noCell_DVP$FDR<0.05)
# FALSE 
# 340 

write.csv(kegg_metal_all_noCell_DVP[kegg_metal_all_noCell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_all_noCell_common_120420.csv')



# Plotting

gg_qqplot(metal_all_noCell_DVP$P.value)
quartz.save('qq_metal_all_noCell_DVP_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_all_noCell_DVP, FDR=T)
quartz.save('manhattan_metal_all_noCell_DVP_120420.png', type = "png", dpi = 300)

volcano_meta(metal_all_noCell_DVP, FDR = TRUE)
quartz.save('volcano_metal_all_noCell_DVP_120420.png', type = "png", dpi = 300)

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_noCell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_noCell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_noCell_DVP_120420.png")

Top 100 probes

X	Name	Effect	StdErr	P.value	Direction	P.FDR	P.Bonf	chr	pos	UCSC_RefGene_Name	UCSC_RefGene_Group
321132	cg23281729	0.9672	0.1110	0.00e+00	-+++	0.0000000	0.0000000	chr18	78005477	PARD6G	TSS200
374163	cg27425262	0.8329	0.1216	0.00e+00	++++	0.0000014	0.0000029	chr2	113953981	PSD4;LOC440839	Body;Body
50934	cg03205258	0.5864	0.0973	0.00e+00	++++	0.0002130	0.0006389	chr22	19929274	TXNRD2;COMT;COMT	1stExon;1stExon;5’UTR
163279	cg11032634	0.6070	0.1118	1.00e-07	++++	0.0053971	0.0215883	chr22	19929254	TXNRD2;COMT	1stExon;TSS200
189046	cg13054212	0.1029	0.0191	1.00e-07	++++	0.0054112	0.0270561	chr4	186356202	C4orf47	Body
309909	cg22387890	0.4666	0.0890	2.00e-07	++++	0.0099055	0.0594328	chr7	6145595	USP42	5’UTR
190387	cg13171197	0.1154	0.0225	3.00e-07	+-++	0.0148622	0.1040357	chr7	90916020
268961	cg18971529	0.3009	0.0592	4.00e-07	++–	0.0150148	0.1381105	chr21	30391563	RWDD2B	1stExon
76120	cg04873963	-0.1042	0.0205	4.00e-07	—-	0.0150148	0.1436575	chr16	2518322
516	cg00026731	-0.1294	0.0255	4.00e-07	—-	0.0150148	0.1501480	chr18	55254092	FECH;FECH	TSS200;TSS200
193559	cg13411311	-0.0993	0.0197	4.00e-07	—-	0.0151489	0.1666382	chr2	241095989
169072	cg11488033	0.3422	0.0683	5.00e-07	-+++	0.0168487	0.2021847	chr3	196705898
2783	cg00156336	-0.1763	0.0354	6.00e-07	—-	0.0181854	0.2364104	chr2	75788423	FAM176A;FAM176A	5’UTR;TSS1500
145256	cg09692492	-0.2570	0.0520	8.00e-07	—-	0.0207220	0.2901074	chr22	23744717	ZDHHC8P	Body
261543	cg18380742	0.0983	0.0200	9.00e-07	+++-	0.0231769	0.3476535	chr1	61674366	NFIA;NFIA;NFIA;NFIA	Body;Body;Body;Body
313664	cg22712983	-0.2239	0.0460	1.10e-06	–+-	0.0262259	0.4196143	chr2	219187374	PNKD;PNKD	TSS1500;Body
237588	cg16511076	0.1075	0.0222	1.30e-06	+++-	0.0280572	0.4769717	chr4	48887480	OCIAD2;OCIAD2	3’UTR;3’UTR
282819	cg20074307	0.0791	0.0165	1.60e-06	+++-	0.0311503	0.5856488	chr14	55092491	SAMD4A;SAMD4A	Body;Body
353609	cg25880954	0.7123	0.1485	1.60e-06	++++	0.0311503	0.6120633	chr1	47900630	MGC12982;FOXD2	TSS1500;TSS1500
291461	cg20805880	0.1020	0.0213	1.70e-06	++++	0.0311503	0.6230065	chr15	73367293	NEO1	Body
124685	cg08207566	0.1017	0.0218	3.00e-06	+++-	0.0544284	1.0000000	chr4	174086461
178342	cg12175949	0.2930	0.0631	3.40e-06	++++	0.0573409	1.0000000	chr22	19929286	TXNRD2;COMT;COMT	1stExon;1stExon;5’UTR
135062	cg08942080	0.1397	0.0301	3.50e-06	++++	0.0573409	1.0000000	chr12	124821568	NCOR2;NCOR2	Body;Body
219690	cg15104380	-0.0789	0.0170	3.70e-06	+—	0.0574026	1.0000000	chr10	99285205	UBTD1	Body
282709	cg20066496	-0.1821	0.0394	3.80e-06	—-	0.0574026	1.0000000	chr15	43213993	TTBK2	TSS1500
93087	cg06039392	0.1254	0.0272	4.10e-06	+++-	0.0584615	1.0000000	chr4	187476953	MTNR1A	TSS1500
309271	cg22336633	-0.1142	0.0248	4.20e-06	—-	0.0584615	1.0000000	chr11	17099688	RPS13	TSS1500
64658	cg04111999	0.0980	0.0214	4.60e-06	++++	0.0616834	1.0000000	chr10	22615540	BMI1	Body
293675	cg21004290	0.1086	0.0238	5.00e-06	++++	0.0651906	1.0000000	chr8	131250320	ASAP1	Body
346588	cg25298319	-0.4235	0.0932	5.60e-06	—-	0.0688970	1.0000000	chr2	233217079
32578	cg02026246	0.1322	0.0291	5.70e-06	+++-	0.0688970	1.0000000	chr11	22687589	GAS2	TSS1500
339841	cg24754507	-0.0947	0.0209	5.90e-06	—-	0.0697038	1.0000000	chr6	28481862	GPX6	Body
268251	cg18907098	0.0729	0.0161	6.20e-06	+++-	0.0713994	1.0000000	chr4	512994	PIGG;PIGG	Body;Body
171628	cg11691429	0.1555	0.0346	7.00e-06	+++-	0.0781339	1.0000000	chr2	947634	SNTG2	Body
92754	cg06013413	0.0904	0.0202	7.40e-06	-+++	0.0795497	1.0000000	chr8	627560	ERICH1	Body
332456	cg24168538	0.2387	0.0534	7.80e-06	++++	0.0795497	1.0000000	chr4	35527016
342170	cg24933709	0.1027	0.0230	7.80e-06	++++	0.0795497	1.0000000	chr7	149120687
23625	cg01445793	0.1780	0.0400	8.70e-06	++++	0.0862942	1.0000000	chr17	3771578	CAMKK1;CAMKK1;CAMKK1	Body;Body;Body
129911	cg08575722	-0.1203	0.0272	1.01e-05	—-	0.0965075	1.0000000	chr11	32421845	WT1;WT1;WT1;WT1	Body;Body;Body;Body
361112	cg26453295	0.0817	0.0185	1.02e-05	++++	0.0965075	1.0000000	chr19	54851740	LILRA4	TSS1500
305009	cg21951425	-0.1306	0.0296	1.06e-05	—-	0.0976511	1.0000000	chr15	26108612	ATP10A	TSS1500
9817	cg00581043	-0.2105	0.0480	1.15e-05	—-	0.1034285	1.0000000	chr6	168106129
173107	cg11797898	-0.1299	0.0297	1.19e-05	—-	0.1034285	1.0000000	chr7	1983375	MAD1L1;MAD1L1;MAD1L1	Body;Body;Body
323330	cg23463533	0.0904	0.0207	1.21e-05	++++	0.1034285	1.0000000	chr7	154473289	DPP6;DPP6;DPP6	Body;Body;Body
126025	cg08293531	-0.1206	0.0276	1.25e-05	—-	0.1038536	1.0000000	chr15	101601180	LRRK1	Body
48009	cg03004999	-0.0716	0.0164	1.27e-05	—-	0.1038536	1.0000000	chr7	43152125	HECW1	TSS200
80568	cg05169951	0.1712	0.0393	1.31e-05	++++	0.1051766	1.0000000	chr16	3017955	KREMEN2;PAQR4;KREMEN2	Body;TSS1500;Body
147224	cg09845489	0.2281	0.0527	1.48e-05	++++	0.1130573	1.0000000	chr7	157667853	PTPRN2;PTPRN2;PTPRN2	Body;Body;Body
156274	cg10502904	0.1329	0.0307	1.50e-05	++++	0.1130573	1.0000000	chr10	131565289	MGMT	3’UTR
90548	cg05872129	0.5015	0.1159	1.50e-05	++++	0.1130573	1.0000000	chr22	39784769
292637	cg20923605	0.2592	0.0599	1.53e-05	++++	0.1130573	1.0000000	chr13	112978683
265757	cg18716164	0.1169	0.0271	1.58e-05	++++	0.1145115	1.0000000	chr19	30019647	VSTM2B	Body
335850	cg24454243	-0.1659	0.0385	1.61e-05	—-	0.1148125	1.0000000	chr7	105221985	EFCAB10	TSS200
38724	cg02415779	0.1107	0.0257	1.64e-05	-++-	0.1148125	1.0000000	chr22	18527778
349119	cg25499746	0.0767	0.0179	1.77e-05	+++-	0.1217128	1.0000000	chr6	16346054	ATXN1;ATXN1	5’UTR;5’UTR
219405	cg15083015	0.1789	0.0417	1.82e-05	++++	0.1226391	1.0000000	chr11	20625714	SLC6A5	Body
339775	cg24748746	-0.2074	0.0485	1.86e-05	—-	0.1232680	1.0000000	chr7	155738916
9019	cg00534624	0.2244	0.0525	1.94e-05	++++	0.1239502	1.0000000	chr16	1845096	IGFALS;IGFALS;IGFALS	TSS200;TSS1500;TSS1500
91411	cg05926928	0.4655	0.1090	1.94e-05	++++	0.1239502	1.0000000	chr17	57297772	GDPD1;GDPD1;GDPD1	TSS200;TSS200;TSS200
95795	cg06239191	0.1902	0.0447	2.08e-05	++++	0.1256788	1.0000000	chr8	145163136	KIAA1875	Body
370181	cg27121095	0.1067	0.0251	2.09e-05	-+++	0.1256788	1.0000000	chr18	77155145	NFATC1;NFATC1;NFATC1	TSS1500;TSS1500;TSS1500
194801	cg13483984	0.1031	0.0243	2.13e-05	+++-	0.1256788	1.0000000	chr1	224580455	WDR26;WDR26	Body;Body
153889	cg10322744	0.4052	0.0953	2.14e-05	++++	0.1256788	1.0000000	chr12	98910138	TMPO;TMPO;TMPO;LOC100128191	Body;Body;Body;TSS200
329980	cg23990236	0.1203	0.0283	2.16e-05	-+++	0.1256788	1.0000000	chr1	12220146
259615	cg18228116	0.2965	0.0700	2.27e-05	-+++	0.1256788	1.0000000	chr10	133995345	JAKMIP3	3’UTR
128672	cg08487455	0.1474	0.0348	2.29e-05	++++	0.1256788	1.0000000	chr16	76311050	CNTNAP4	TSS200
131033	cg08654960	-0.1347	0.0319	2.36e-05	—-	0.1256788	1.0000000	chr16	85319859
12204	cg00729699	-0.0920	0.0218	2.36e-05	—-	0.1256788	1.0000000	chr8	21918075	EPB49;EPB49;EPB49;EPB49;EPB49;EPB49	5’UTR;5’UTR;5’UTR;5’UTR;5’UTR;5’UTR
235393	cg16353272	0.0828	0.0196	2.36e-05	++++	0.1256788	1.0000000	chr16	2124240	TSC2;TSC2;TSC2	Body;Body;Body
91432	cg05927817	0.3361	0.0795	2.36e-05	++++	0.1256788	1.0000000	chr6	18020357
80361	cg05157266	0.1310	0.0310	2.38e-05	+++-	0.1256788	1.0000000	chr2	183901614	NCKAP1;NCKAP1	Body;Body
193732	cg13423098	0.1356	0.0321	2.40e-05	+++-	0.1256788	1.0000000	chr15	23807234
277830	cg19702802	0.1563	0.0370	2.46e-05	++++	0.1262596	1.0000000	chr19	46417729	NANOS2	1stExon
159378	cg10729167	0.1354	0.0321	2.48e-05	++++	0.1262596	1.0000000	chr10	111220101
337433	cg24577193	-0.3193	0.0759	2.57e-05	—-	0.1274285	1.0000000	chr1	78148396	ZZZ3	TSS200
269647	cg19029220	-0.0802	0.0191	2.61e-05	+—	0.1274285	1.0000000	chr2	64067822	UGP2;UGP2	TSS1500;TSS1500
321501	cg23313031	-0.0993	0.0236	2.63e-05	—-	0.1274285	1.0000000	chr6	29974745	HLA-J;NCRNA00171	Body;Body
320947	cg23268677	0.2321	0.0552	2.63e-05	++++	0.1274285	1.0000000	chr22	19929097	TXNRD2;COMT	Body;TSS200
196530	cg13587236	0.0881	0.0210	2.71e-05	+++-	0.1294457	1.0000000	chr9	128472496
64158	cg04080724	0.1031	0.0246	2.82e-05	++++	0.1327804	1.0000000	chr4	140202327	C4orf49	TSS1500
162593	cg10980774	0.1419	0.0341	3.12e-05	++++	0.1450755	1.0000000	chr11	112832547	NCAM1;NCAM1;NCAM1	Body;Body;Body
4028	cg00238318	-0.1141	0.0274	3.18e-05	–+-	0.1450755	1.0000000	chr10	94607950	EXOC6;EXOC6	Body;TSS1500
39898	cg02492873	0.1026	0.0247	3.19e-05	++–	0.1450755	1.0000000	chr2	25193821	DNAJC27	Body
348207	cg25423077	0.3801	0.0915	3.26e-05	++++	0.1463134	1.0000000	chr18	59221601	CDH20	Body
338787	cg24682751	-0.1872	0.0451	3.36e-05	—-	0.1488781	1.0000000	chr15	93591750	RGMA;RGMA;RGMA;RGMA;RGMA;RGMA	Body;Body;Body;Body;Body;Body
190991	cg13221086	0.0873	0.0211	3.39e-05	+++-	0.1488781	1.0000000	chr3	31809318	OSBPL10	Body
95484	cg06216157	-0.0646	0.0156	3.47e-05	–+-	0.1506368	1.0000000	chr17	7210363	EIF5A;EIF5A;EIF5A;EIF5A;EIF5A	TSS1500;5’UTR;TSS1500;TSS1500;1stExon
179110	cg12235073	0.1005	0.0243	3.57e-05	++++	0.1528272	1.0000000	chr10	6270423	PFKFB3;PFKFB3	Body;Body
167176	cg11332363	0.1782	0.0431	3.64e-05	++-+	0.1528272	1.0000000	chr19	54023999	ZNF331	TSS200
304836	cg21936789	0.1721	0.0417	3.64e-05	++++	0.1528272	1.0000000	chr3	47620545	CSPG5	TSS200
5926	cg00353112	-0.0979	0.0238	3.82e-05	—-	0.1570929	1.0000000	chr15	45879221	PLDN	TSS200
69221	cg04406454	-0.1479	0.0359	3.83e-05	—-	0.1570929	1.0000000	chr6	10398494	TFAP2A;TFAP2A;TFAP2A	3’UTR;3’UTR;3’UTR
110491	cg07219314	-0.1410	0.0343	3.88e-05	—-	0.1573107	1.0000000	chr22	23744725	ZDHHC8P	Body
295936	cg21185289	0.2772	0.0675	4.02e-05	++++	0.1613376	1.0000000	chr2	74743437	TLX2	3’UTR
107294	cg07019740	0.2793	0.0681	4.07e-05	++++	0.1616651	1.0000000	chr22	19929205	TXNRD2;COMT	Body;TSS200
362881	cg26580480	-0.0960	0.0234	4.18e-05	—-	0.1643442	1.0000000	chr6	43241339	TTBK1	Body
229928	cg15931233	0.0783	0.0191	4.34e-05	++++	0.1680165	1.0000000	chr5	53455496	ARL15	Body
135334	cg08963616	0.0861	0.0211	4.37e-05	++++	0.1680165	1.0000000	chr8	17249585	MTMR7	Body
59640	cg03770962	0.0905	0.0221	4.41e-05	+++-	0.1680165	1.0000000	chr7	148477754	CUL1	Body
87925	cg05677467	0.0620	0.0152	4.50e-05	++-+	0.1698457	1.0000000	chr15	85197654	WDR73	TSS200

---

Top 100 GO terms

X	ONTOLOGY	TERM	N	DE	P.DE	FDR
GO:0034156	BP	negative regulation of toll-like receptor 7 signaling pathway	1	1	0.0006729	1
GO:0004325	MF	ferrochelatase activity	1	1	0.0008725	1
GO:0042053	BP	regulation of dopamine metabolic process	18	2	0.0013589	1
GO:0042069	BP	regulation of catecholamine metabolic process	18	2	0.0013589	1
GO:0048609	BP	multicellular organismal reproductive process	753	6	0.0016644	1
GO:0032504	BP	multicellular organism reproduction	768	6	0.0017622	1
GO:0032997	CC	Fc receptor complex	3	1	0.0019011	1
GO:0032998	CC	Fc-epsilon receptor I complex	3	1	0.0019011	1
GO:0034155	BP	regulation of toll-like receptor 7 signaling pathway	3	1	0.0019833	1
GO:0042417	BP	dopamine metabolic process	33	2	0.0038976	1
GO:0031337	BP	positive regulation of sulfur amino acid metabolic process	1	1	0.0048329	1
GO:0050668	BP	positive regulation of homocysteine metabolic process	1	1	0.0048329	1
GO:1904527	BP	negative regulation of microtubule binding	2	1	0.0049443	1
GO:0050666	BP	regulation of homocysteine metabolic process	2	1	0.0055603	1
GO:1902816	BP	regulation of protein localization to microtubule	5	1	0.0055794	1
GO:1902817	BP	negative regulation of protein localization to microtubule	5	1	0.0055794	1
GO:0051267	MF	CP2 mannose-ethanolamine phosphotransferase activity	1	1	0.0057471	1
GO:0072299	BP	negative regulation of metanephric glomerulus development	1	1	0.0058507	1
GO:0072302	BP	negative regulation of metanephric glomerular mesangial cell proliferation	1	1	0.0058507	1
GO:0006584	BP	catecholamine metabolic process	46	2	0.0058803	1
GO:0009712	BP	catechol-containing compound metabolic process	46	2	0.0058803	1
GO:0008502	MF	melatonin receptor activity	3	1	0.0059440	1
GO:0001544	BP	initiation of primordial ovarian follicle growth	2	1	0.0062992	1
GO:0031335	BP	regulation of sulfur amino acid metabolic process	3	1	0.0063248	1
GO:0016036	BP	cellular response to phosphate starvation	2	1	0.0064527	1
GO:0034154	BP	toll-like receptor 7 signaling pathway	6	1	0.0069035	1
GO:0016209	MF	antioxidant activity	83	2	0.0069530	1
GO:0021935	BP	cerebellar granule cell precursor tangential migration	2	1	0.0070459	1
GO:0016206	MF	catechol O-methyltransferase activity	2	1	0.0071794	1
GO:0102084	MF	L-dopa O-methyltransferase activity	2	1	0.0071794	1
GO:0102938	MF	orcinol O-methyltransferase activity	2	1	0.0071794	1
GO:0072301	BP	regulation of metanephric glomerular mesangial cell proliferation	2	1	0.0072438	1
GO:0051377	MF	mannose-ethanolamine phosphotransferase activity	3	1	0.0072565	1
GO:0045764	BP	positive regulation of cellular amino acid metabolic process	3	1	0.0074539	1
GO:0042698	BP	ovulation cycle	69	2	0.0075994	1
GO:0035814	BP	negative regulation of renal sodium excretion	3	1	0.0078159	1
GO:0061032	BP	visceral serous pericardium development	2	1	0.0078660	1
GO:0033238	BP	regulation of cellular amine metabolic process	78	2	0.0080612	1
GO:0046501	BP	protoporphyrinogen IX metabolic process	10	1	0.0081033	1
GO:0004416	MF	hydroxyacylglutathione hydrolase activity	2	1	0.0083624	1
GO:0019243	BP	methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione	2	1	0.0083624	1
GO:0051596	BP	methylglyoxal catabolic process	2	1	0.0083624	1
GO:0061727	BP	methylglyoxal catabolic process to lactate	2	1	0.0083624	1
GO:0072262	BP	metanephric glomerular mesangial cell proliferation involved in metanephros development	3	1	0.0088988	1
GO:0051176	BP	positive regulation of sulfur metabolic process	3	1	0.0090728	1
GO:0072166	BP	posterior mesonephric tubule development	2	1	0.0095614	1
GO:0021934	BP	hindbrain tangential cell migration	3	1	0.0097382	1
GO:0070181	MF	small ribosomal subunit rRNA binding	10	1	0.0101955	1
GO:0035801	BP	adrenal cortex development	2	1	0.0103000	1
GO:0035802	BP	adrenal cortex formation	2	1	0.0103000	1
GO:0098869	BP	cellular oxidant detoxification	96	2	0.0105889	1
GO:2001074	BP	regulation of metanephric ureteric bud development	2	1	0.0107573	1
GO:2001076	BP	positive regulation of metanephric ureteric bud development	2	1	0.0107573	1
GO:1990748	BP	cellular detoxification	105	2	0.0114517	1
GO:1905643	BP	positive regulation of DNA methylation	3	1	0.0119423	1
GO:0016013	CC	syntrophin complex	3	1	0.0122287	1
GO:1903527	BP	positive regulation of membrane tubulation	4	1	0.0122956	1
GO:0034164	BP	negative regulation of toll-like receptor 9 signaling pathway	3	1	0.0125471	1
GO:0009438	BP	methylglyoxal metabolic process	5	1	0.0125610	1
GO:0032687	BP	negative regulation of interferon-alpha production	6	1	0.0126305	1
GO:0044729	MF	hemi-methylated DNA-binding	3	1	0.0131488	1
GO:0042420	BP	dopamine catabolic process	5	1	0.0131948	1
GO:0010385	MF	double-stranded methylated DNA binding	4	1	0.0132070	1
GO:0044106	BP	cellular amine metabolic process	119	2	0.0137636	1
GO:0042182	BP	ketone catabolic process	9	1	0.0140733	1
GO:0071535	MF	RING-like zinc finger domain binding	4	1	0.0142495	1
GO:0036353	BP	histone H2A-K119 monoubiquitination	8	1	0.0144099	1
GO:0072223	BP	metanephric glomerular mesangium development	5	1	0.0144316	1
GO:2000195	BP	negative regulation of female gonad development	5	1	0.0144413	1
GO:0045914	BP	negative regulation of catecholamine metabolic process	4	1	0.0147543	1
GO:0045963	BP	negative regulation of dopamine metabolic process	4	1	0.0147543	1
GO:1903525	BP	regulation of membrane tubulation	6	1	0.0153190	1
GO:0009308	BP	amine metabolic process	128	2	0.0153320	1
GO:0072125	BP	negative regulation of glomerular mesangial cell proliferation	4	1	0.0154115	1
GO:0090194	BP	negative regulation of glomerulus development	4	1	0.0154115	1
GO:0019614	BP	catechol-containing compound catabolic process	6	1	0.0155222	1
GO:0042424	BP	catecholamine catabolic process	6	1	0.0155222	1
GO:0098754	BP	detoxification	129	2	0.0158916	1
GO:0007356	BP	thorax and anterior abdomen determination	5	1	0.0168477	1
GO:0007614	BP	short-term memory	9	1	0.0176631	1
GO:0001547	BP	antral ovarian follicle growth	8	1	0.0178660	1
GO:0008585	BP	female gonad development	92	2	0.0180206	1
GO:0034163	BP	regulation of toll-like receptor 9 signaling pathway	8	1	0.0185349	1
GO:0044703	BP	multi-organism reproductive process	911	5	0.0185365	1
GO:1905940	BP	negative regulation of gonad development	6	1	0.0186027	1
GO:0019336	BP	phenol-containing compound catabolic process	9	1	0.0187532	1
GO:0072298	BP	regulation of metanephric glomerulus development	5	1	0.0188366	1
GO:0046185	BP	aldehyde catabolic process	11	1	0.0190056	1
GO:0035502	BP	metanephric part of ureteric bud development	6	1	0.0190321	1
GO:0004791	MF	thioredoxin-disulfide reductase activity	7	1	0.0191359	1
GO:0051537	MF	2 iron, 2 sulfur cluster binding	21	1	0.0194764	1
GO:0018958	BP	phenol-containing compound metabolic process	94	2	0.0196449	1
GO:0046545	BP	development of primary female sexual characteristics	96	2	0.0201548	1
GO:0033240	BP	positive regulation of cellular amine metabolic process	7	1	0.0210294	1
GO:0016668	MF	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor	11	1	0.0220457	1
GO:0072284	BP	metanephric S-shaped body morphogenesis	6	1	0.0220657	1
GO:0048511	BP	rhythmic process	286	3	0.0222464	1
GO:0007354	BP	zygotic determination of anterior/posterior axis, embryo	6	1	0.0227852	1
GO:0035372	BP	protein localization to microtubule	14	1	0.0228225	1
GO:0033239	BP	negative regulation of cellular amine metabolic process	7	1	0.0229552	1

With cell type adjustment

Blood only

metal_blood_cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/blood_cell_common_DVP_1204201.tbl', sep = "\t")

metal_blood_cell_DVP = metalProcess(metal_blood_cell_DVP)

write.csv(metal_blood_cell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_blood_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_blood_cell_DVP$P.value < 0.05)
#  FALSE   TRUE 
# 348773  28578 

# FDR
table(metal_blood_cell_DVP$P.FDR < 0.05)
#  FALSE   TRUE 
# 377328     23 

table(metal_blood_cell_DVP$P.FDR < 0.1)
#  FALSE   TRUE 
# 377266     85 

# Bonferroni
table(metal_blood_cell_DVP$P.Bonf < 0.05)
#  FALSE   TRUE 
#  377347      4 


# GO analysis, FDR < 0.1 probes

go_metal_blood_cell_DVP = gometh(sig.cpg = metal_blood_cell_DVP$Name[metal_blood_cell_DVP$P.FDR < 0.1], all.cpg = metal_blood_cell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_blood_cell_DVP = go_metal_blood_cell_DVP[order(go_metal_blood_cell_DVP$P.DE),]

table(go_metal_blood_cell_DVP$P.DE<0.05)
# FALSE  TRUE 
# 22282   301 

table(go_metal_blood_cell_DVP$FDR<0.05)
# FALSE 
# 22583 

write.csv(go_metal_blood_cell_DVP[go_metal_blood_cell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_blood_cell_common_120420.csv')


# KEGG analysis, FDR < 0.1 probes

kegg_metal_blood_cell_DVP = gometh(sig.cpg = metal_blood_cell_DVP$Name[metal_blood_cell_DVP$P.FDR < 0.1], all.cpg = metal_blood_cell_DVP$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_blood_cell_DVP = kegg_metal_blood_cell_DVP[order(kegg_metal_blood_cell_DVP$P.DE),]

table(kegg_metal_blood_cell_DVP$P.DE<0.05)
# FALSE  TRUE 
# 335     5 

table(kegg_metal_blood_cell_DVP$FDR<0.05)
# FALSE 
# 340 

write.csv(kegg_metal_blood_cell_DVP[kegg_metal_blood_cell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_blood_cell_common_120420.csv')




# Plotting

gg_qqplot(metal_blood_cell_DVP$P.value)
quartz.save('qq_metal_blood_cell_DVP_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_blood_cell_DVP, FDR=T)
quartz.save('manhattan_metal_blood_cell_DVP_120420.png', type = "png", dpi = 300)

volcano_meta(metal_blood_cell_DVP, FDR = TRUE)
quartz.save('volcano_metal_blood_cell_DVP_120420.png', type = "png", dpi = 300)

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_blood_cell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_blood_cell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_blood_cell_DVP_120420.png")

Top 100 probes

X	Name	Effect	StdErr	P.value	Direction	P.FDR	P.Bonf	chr	pos	UCSC_RefGene_Name	UCSC_RefGene_Group
321132	cg23281729	0.9728	0.1462	0.00e+00	-++	0.0000108	0.0000108	chr18	78005477	PARD6G	TSS200
374163	cg27425262	0.8238	0.1473	0.00e+00	+++	0.0042584	0.0085168	chr2	113953981	PSD4;LOC440839	Body;Body
167567	cg11361658	0.1740	0.0323	1.00e-07	+++	0.0087332	0.0261995	chr5	128452311
50934	cg03205258	0.6862	0.1287	1.00e-07	+++	0.0091725	0.0366898	chr22	19929274	TXNRD2;COMT;COMT	1stExon;1stExon;5’UTR
145256	cg09692492	-0.3502	0.0664	1.00e-07	—	0.0102489	0.0512443	chr22	23744717	ZDHHC8P	Body
163279	cg11032634	0.7694	0.1503	3.00e-07	+++	0.0192135	0.1152807	chr22	19929254	TXNRD2;COMT	1stExon;TSS200
237588	cg16511076	0.1302	0.0257	4.00e-07	+++	0.0219295	0.1535064	chr4	48887480	OCIAD2;OCIAD2	3’UTR;3’UTR
309909	cg22387890	0.5501	0.1098	5.00e-07	+++	0.0228562	0.2051280	chr7	6145595	USP42	5’UTR
314099	cg22749736	0.1312	0.0262	6.00e-07	+++	0.0228562	0.2087506	chr11	1306759	TOLLIP	Body
64158	cg04080724	0.1387	0.0278	6.00e-07	+++	0.0228562	0.2285615	chr4	140202327	C4orf49	TSS1500
80568	cg05169951	0.2307	0.0465	7.00e-07	+++	0.0239892	0.2638816	chr16	3017955	KREMEN2;PAQR4;KREMEN2	Body;TSS1500;Body
11224	cg00668103	0.1440	0.0292	8.00e-07	+++	0.0254209	0.3050505	chr7	100084730	C7orf51	Body
124685	cg08207566	0.1245	0.0255	1.00e-06	+++	0.0303042	0.3939544	chr4	174086461
18303	cg01101647	0.1337	0.0275	1.10e-06	+++	0.0303228	0.4245199	chr4	66535732	EPHA5;EPHA5	TSS200;TSS200
116190	cg07611790	0.1053	0.0217	1.30e-06	+++	0.0309847	0.4724435	chr19	49240823	RASIP1	Body
171628	cg11691429	0.2056	0.0426	1.40e-06	+++	0.0309847	0.5248952	chr2	947634	SNTG2	Body
295936	cg21185289	0.3802	0.0789	1.50e-06	+++	0.0309847	0.5471590	chr2	74743437	TLX2	3’UTR
125889	cg08285768	0.1113	0.0231	1.50e-06	+++	0.0309847	0.5577248	chr15	86038622	AKAP13;AKAP13	Body;Body
202666	cg13972353	0.1460	0.0304	1.60e-06	+++	0.0311811	0.5924411	chr9	139354348	SEC16A	Body
102811	cg06740986	0.1067	0.0225	2.10e-06	+++	0.0392634	0.7852674	chr1	184838417	FAM129A	Body
303849	cg21857098	0.1220	0.0259	2.50e-06	+++	0.0428636	0.9286608	chr15	25638137	UBE3A;UBE3A;UBE3A	Body;Body;Body
55105	cg03479942	0.1266	0.0269	2.50e-06	+++	0.0428636	0.9430001	chr16	69341763	SNTB2	3’UTR
121453	cg07984508	0.1050	0.0224	2.70e-06	+++	0.0447243	1.0000000	chr15	77426719	SGK269	Body
168599	cg11440940	0.1144	0.0246	3.30e-06	+++	0.0509569	1.0000000	chr19	8510764	HNRNPM;HNRNPM	Body;Body
150964	cg10117884	0.1325	0.0285	3.40e-06	+++	0.0509569	1.0000000	chr1	166955898
308533	cg22267402	0.1390	0.0300	3.50e-06	+++	0.0509569	1.0000000	chr22	44463707	PARVB;PARVB	Body;Body
100415	cg06581201	0.2001	0.0434	4.00e-06	+++	0.0529265	1.0000000	chr6	168534038
248409	cg17332762	0.1085	0.0236	4.20e-06	+++	0.0529265	1.0000000	chr3	106967639	LOC344595;LOC344595	Body;Body
93087	cg06039392	0.1497	0.0325	4.20e-06	+++	0.0529265	1.0000000	chr4	187476953	MTNR1A	TSS1500
58507	cg03700279	0.1118	0.0243	4.20e-06	+++	0.0529265	1.0000000	chr2	44576358	PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;PREPL	Body;Body;5’UTR;5’UTR;Body;Body;Body
32578	cg02026246	0.1671	0.0364	4.30e-06	+++	0.0529265	1.0000000	chr11	22687589	GAS2	TSS1500
373469	cg27371984	0.2504	0.0547	4.80e-06	+++	0.0561545	1.0000000	chr17	78009155	CCDC40;TBC1D16	TSS1500;5’UTR
156274	cg10502904	0.1806	0.0396	5.10e-06	+++	0.0582035	1.0000000	chr10	131565289	MGMT	3’UTR
208658	cg14332223	0.1916	0.0421	5.30e-06	–+	0.0592108	1.0000000	chr19	56136067	ZNF784	TSS200
129911	cg08575722	-0.1446	0.0318	5.50e-06	—	0.0595244	1.0000000	chr11	32421845	WT1;WT1;WT1;WT1	Body;Body;Body;Body
120767	cg07935287	-0.1377	0.0304	5.80e-06	—	0.0605019	1.0000000	chr18	54318347	WDR7;WDR7	TSS1500;TSS1500
25526	cg01570086	-0.1467	0.0325	6.20e-06	—	0.0633032	1.0000000	chr15	74833080	ARID3B	TSS1500
110491	cg07219314	-0.1929	0.0428	6.60e-06	—	0.0645540	1.0000000	chr22	23744725	ZDHHC8P	Body
199880	cg13797228	0.1106	0.0246	7.00e-06	-++	0.0645540	1.0000000	chr3	126076243	KLF15	TSS200
214646	cg14718822	-0.1749	0.0389	7.10e-06	-+-	0.0645540	1.0000000	chr6	84234250	PRSS35;PRSS35	Body;Body
156000	cg10485752	0.1511	0.0337	7.20e-06	+++	0.0645540	1.0000000	chr1	26021655	MAN1C1	Body
109701	cg07168204	0.1274	0.0284	7.20e-06	+++	0.0645540	1.0000000	chr5	149864599
10618	cg00629117	0.7703	0.1719	7.40e-06	+++	0.0650448	1.0000000	chr16	1844932	IGFALS;IGFALS;IGFALS	TSS200;TSS1500;TSS1500
11047	cg00657529	0.0977	0.0219	8.00e-06	+++	0.0684034	1.0000000	chr6	31698687	CLIC1;DDAH2	Body;TSS1500
227727	cg15754901	0.1165	0.0261	8.30e-06	+-+	0.0692900	1.0000000	chr17	5402972	LOC728392	3’UTR
320947	cg23268677	0.3213	0.0723	8.70e-06	+++	0.0717705	1.0000000	chr22	19929097	TXNRD2;COMT	Body;TSS200
293675	cg21004290	0.1299	0.0293	9.00e-06	+++	0.0719697	1.0000000	chr8	131250320	ASAP1	Body
324700	cg23574838	0.0719	0.0163	1.01e-05	+++	0.0778535	1.0000000	chr20	3186475	DDRGK1	TSS1500
132616	cg08770961	0.3268	0.0741	1.03e-05	+++	0.0778535	1.0000000	chr16	66956122	RRAD;RRAD	Body;Body
316511	cg22938135	0.0961	0.0218	1.06e-05	+++	0.0778535	1.0000000	chr5	175841493	CLTB;CLTB	Body;Body
107264	cg07018132	0.0975	0.0222	1.10e-05	+++	0.0778535	1.0000000	chr16	718091	RHOT2	TSS200
281026	cg19929852	0.1226	0.0279	1.10e-05	+++	0.0778535	1.0000000	chr4	15068643	CPEB2;CPEB2	3’UTR;3’UTR
351734	cg25721832	0.0929	0.0212	1.12e-05	+++	0.0778535	1.0000000	chr3	81913557
268961	cg18971529	0.3043	0.0693	1.15e-05	++-	0.0778535	1.0000000	chr21	30391563	RWDD2B	1stExon
198387	cg13698261	0.1019	0.0232	1.15e-05	+++	0.0778535	1.0000000	chr9	97841956	C9orf3	Body
109543	cg07159858	-0.1358	0.0310	1.16e-05	+–	0.0778535	1.0000000	chr14	75744601	FOS	TSS1500
62770	cg03988518	0.1819	0.0415	1.18e-05	++-	0.0778535	1.0000000	chr6	170763536
149284	cg09996597	0.4310	0.0985	1.22e-05	+++	0.0781745	1.0000000	chr16	1844927	IGFALS;IGFALS;IGFALS	TSS200;TSS1500;TSS1500
51985	cg03277137	0.0799	0.0183	1.22e-05	+++	0.0781745	1.0000000	chr13	113513653	ATP11A;ATP11A	Body;Body
120984	cg07952047	0.1885	0.0431	1.24e-05	+++	0.0781745	1.0000000	chr19	54024110	ZNF331	TSS200
35145	cg02192228	0.1987	0.0455	1.29e-05	+++	0.0791857	1.0000000	chr3	8809536	OXTR	Body
178342	cg12175949	0.3943	0.0906	1.35e-05	+++	0.0791857	1.0000000	chr22	19929286	TXNRD2;COMT;COMT	1stExon;1stExon;5’UTR
259615	cg18228116	0.3740	0.0860	1.36e-05	-++	0.0791857	1.0000000	chr10	133995345	JAKMIP3	3’UTR
114654	cg07510163	0.1646	0.0378	1.36e-05	+++	0.0791857	1.0000000	chr2	44547313	PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;SLC3A1;PREPL	3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;Body;3’UTR
282819	cg20074307	0.0870	0.0200	1.36e-05	+++	0.0791857	1.0000000	chr14	55092491	SAMD4A;SAMD4A	Body;Body
169144	cg11494866	0.1107	0.0255	1.39e-05	+++	0.0794152	1.0000000	chr8	42695070	THAP1;THAP1	Body;Body
271236	cg19170881	-0.1888	0.0435	1.42e-05	—	0.0802012	1.0000000	chr7	101129980	EMID2	Body
351392	cg25691442	0.1096	0.0253	1.46e-05	+++	0.0812969	1.0000000	chr15	63345512	TPM1;TPM1;TPM1;TPM1;TPM1;TPM1;TPM1	Body;Body;Body;Body;Body;Body;Body
138885	cg09235788	0.1447	0.0335	1.57e-05	+++	0.0859704	1.0000000	chr1	111220207
370643	cg27155653	-0.1124	0.0261	1.61e-05	—	0.0867907	1.0000000	chr1	183604774	ARPC5;RGL1	1stExon;TSS1500
351214	cg25674826	0.2883	0.0670	1.71e-05	+++	0.0906705	1.0000000	chr21	35446543	MRPS6;SLC5A3	Body;5’UTR
148318	cg09920145	-0.1037	0.0241	1.76e-05	—	0.0923986	1.0000000	chr3	69100714	TMF1	Body
232066	cg16101346	0.1755	0.0409	1.79e-05	-++	0.0924251	1.0000000	chr1	186650479	PTGS2	TSS1500
343712	cg25052374	0.0833	0.0194	1.83e-05	+++	0.0935728	1.0000000	chr17	76991253	CANT1;CANT1;CANT1	Body;Body;Body
207024	cg14231959	0.1401	0.0327	1.90e-05	+++	0.0940895	1.0000000	chr8	1897035	ARHGEF10	Body
222184	cg15317815	0.2440	0.0570	1.90e-05	+++	0.0940895	1.0000000	chr3	8809306	OXTR	Body
349119	cg25499746	0.0878	0.0205	1.94e-05	+++	0.0949748	1.0000000	chr6	16346054	ATXN1;ATXN1	5’UTR;5’UTR
114218	cg07479711	0.1174	0.0275	1.98e-05	+++	0.0953886	1.0000000	chr5	1524940	LPCAT1	TSS1500
26498	cg01632803	0.1085	0.0254	2.00e-05	+++	0.0953886	1.0000000	chr19	48891159	KDELR1	Body
127440	cg08400962	0.1223	0.0287	2.04e-05	+++	0.0955490	1.0000000	chr19	34112316	CHST8;CHST8	TSS1500;TSS1500
64658	cg04111999	0.1037	0.0244	2.05e-05	+++	0.0955490	1.0000000	chr10	22615540	BMI1	Body
265593	cg18703721	0.1274	0.0299	2.10e-05	+++	0.0966387	1.0000000	chr10	75282672	USP54	Body
41686	cg02608453	0.1053	0.0248	2.20e-05	+++	0.0986884	1.0000000	chr9	125241447	OR1J1	TSS1500
161566	cg10898607	-0.1150	0.0271	2.20e-05	—	0.0986884	1.0000000	chr3	101405733	RPL24	TSS200
377087	cg27647852	0.0989	0.0233	2.22e-05	+++	0.0986884	1.0000000	chr20	44036899	DBNDD2;DBNDD2;DBNDD2;SYS1-DBNDD2;DBNDD2;DBNDD2;DBNDD2	5’UTR;5’UTR;TSS200;Body;5’UTR;5’UTR;TSS200
181408	cg12433479	0.1713	0.0405	2.38e-05	+++	0.1031703	1.0000000	chr3	38683662	SCN5A;SCN5A;SCN5A;SCN5A;SCN5A;SCN5A	5’UTR;5’UTR;5’UTR;5’UTR;5’UTR;5’UTR
111585	cg07297467	0.1250	0.0296	2.42e-05	+++	0.1031703	1.0000000	chr2	101635691	RPL31;TBC1D8	3’UTR;Body
317171	cg22988651	0.1333	0.0316	2.43e-05	+++	0.1031703	1.0000000	chr3	15792635	ANKRD28	Body
26185	cg01614020	0.2810	0.0666	2.44e-05	+++	0.1031703	1.0000000	chr8	24814137	NEFL	TSS200
190817	cg13208054	0.0820	0.0194	2.47e-05	+++	0.1031703	1.0000000	chr17	25936354	KSR1	Body
153219	cg10273420	-0.0916	0.0217	2.49e-05	-+-	0.1031703	1.0000000	chr10	43953760	ZNF487	Body
308465	cg22261158	0.1292	0.0307	2.53e-05	+++	0.1037305	1.0000000	chr12	98941654	TMPO;TMPO	3’UTR;3’UTR
201631	cg13909585	0.2349	0.0559	2.61e-05	+++	0.1041717	1.0000000	chr7	82792379	PCLO;PCLO	TSS200;TSS200
240114	cg16681246	0.0937	0.0223	2.62e-05	+++	0.1041717	1.0000000	chr2	65541310	SPRED2;SPRED2	Body;Body
131033	cg08654960	-0.1464	0.0348	2.63e-05	—	0.1041717	1.0000000	chr16	85319859
31762	cg01972350	-0.1407	0.0335	2.68e-05	—	0.1041717	1.0000000	chr17	79155695	LOC388428	Body
150911	cg10114235	0.1228	0.0293	2.69e-05	+++	0.1041717	1.0000000	chr6	169449059
47856	cg02996181	0.0722	0.0172	2.71e-05	++-	0.1041717	1.0000000	chr11	417643	SIGIRR;SIGIRR	TSS1500;TSS1500
199205	cg13751796	0.0845	0.0202	2.73e-05	+++	0.1041717	1.0000000	chr9	132633833	USP20;USP20;USP20	Body;Body;Body
229928	cg15931233	0.1027	0.0245	2.77e-05	+++	0.1046017	1.0000000	chr5	53455496	ARL15	Body

---

Top 100 GO terms

X	ONTOLOGY	TERM	N	DE	P.DE	FDR
GO:0048545	BP	response to steroid hormone	329	8	0.0002538	1
GO:2000171	BP	negative regulation of dendrite development	25	3	0.0006726	1
GO:0003044	BP	regulation of systemic arterial blood pressure mediated by a chemical signal	45	3	0.0009954	1
GO:0070972	BP	protein localization to endoplasmic reticulum	134	4	0.0011312	1
GO:0009725	BP	response to hormone	863	12	0.0013203	1
GO:0032570	BP	response to progesterone	45	3	0.0015462	1
GO:0031307	CC	integral component of mitochondrial outer membrane	19	2	0.0030355	1
GO:0099631	CC	postsynaptic endocytic zone cytoplasmic component	2	1	0.0031890	1
GO:0031306	CC	intrinsic component of mitochondrial outer membrane	20	2	0.0034739	1
GO:0071383	BP	cellular response to steroid hormone stimulus	194	5	0.0035536	1
GO:0030728	BP	ovulation	20	2	0.0035557	1
GO:0050774	BP	negative regulation of dendrite morphogenesis	14	2	0.0039691	1
GO:0006979	BP	response to oxidative stress	434	7	0.0040529	1
GO:0061000	BP	negative regulation of dendritic spine development	11	2	0.0041920	1
GO:0004990	MF	oxytocin receptor activity	1	1	0.0046387	1
GO:0006305	BP	DNA alkylation	71	3	0.0047397	1
GO:0006306	BP	DNA methylation	71	3	0.0047397	1
GO:0016010	CC	dystrophin-associated glycoprotein complex	18	2	0.0047560	1
GO:0090665	CC	glycoprotein complex	18	2	0.0047560	1
GO:0061318	BP	renal filtration cell differentiation	18	2	0.0051905	1
GO:0072112	BP	glomerular visceral epithelial cell differentiation	18	2	0.0051905	1
GO:0050886	BP	endocrine process	78	3	0.0054921	1
GO:0010335	BP	response to non-ionic osmotic stress	1	1	0.0056612	1
GO:0071471	BP	cellular response to non-ionic osmotic stress	1	1	0.0056612	1
GO:0007613	BP	memory	116	4	0.0056747	1
GO:1903524	BP	positive regulation of blood circulation	72	3	0.0056822	1
GO:0072311	BP	glomerular epithelial cell differentiation	19	2	0.0057171	1
GO:0044703	BP	multi-organism reproductive process	943	10	0.0062853	1
GO:0072010	BP	glomerular epithelium development	22	2	0.0066983	1
GO:0043401	BP	steroid hormone mediated signaling pathway	131	4	0.0067175	1
GO:0004666	MF	prostaglandin-endoperoxide synthase activity	2	1	0.0070536	1
GO:0090362	BP	positive regulation of platelet-derived growth factor production	2	1	0.0073248	1
GO:0034643	BP	establishment of mitochondrion localization, microtubule-mediated	22	2	0.0074343	1
GO:0047497	BP	mitochondrion transport along microtubule	22	2	0.0074343	1
GO:0030371	MF	translation repressor activity	24	2	0.0079009	1
GO:0003073	BP	regulation of systemic arterial blood pressure	87	3	0.0079262	1
GO:0051654	BP	establishment of mitochondrion localization	25	2	0.0086020	1
GO:0001990	BP	regulation of systemic arterial blood pressure by hormone	35	2	0.0087258	1
GO:0007565	BP	female pregnancy	175	4	0.0088200	1
GO:0008217	BP	regulation of blood pressure	175	4	0.0088372	1
GO:0044728	BP	DNA methylation or demethylation	94	3	0.0091241	1
GO:2000815	BP	regulation of mRNA stability involved in response to oxidative stress	2	1	0.0091562	1
GO:0030660	CC	Golgi-associated vesicle membrane	103	3	0.0091582	1
GO:0035037	BP	sperm entry	1	1	0.0093095	1
GO:0061795	BP	Golgi lumen acidification	1	1	0.0093095	1
GO:1905526	BP	regulation of Golgi lumen acidification	1	1	0.0093095	1
GO:1905528	BP	positive regulation of Golgi lumen acidification	1	1	0.0093095	1
GO:0030431	BP	sleep	34	2	0.0098816	1
GO:0045987	BP	positive regulation of smooth muscle contraction	31	2	0.0099122	1
GO:0031337	BP	positive regulation of sulfur amino acid metabolic process	1	1	0.0099457	1
GO:0050668	BP	positive regulation of homocysteine metabolic process	1	1	0.0099457	1
GO:0045777	BP	positive regulation of blood pressure	37	2	0.0099634	1
GO:0051704	BP	multi-organism process	1013	10	0.0100226	1
GO:0003065	BP	positive regulation of heart rate by epinephrine	1	1	0.0103331	1
GO:0001992	BP	regulation of systemic arterial blood pressure by vasopressin	4	1	0.0107040	1
GO:1905550	BP	regulation of protein localization to endoplasmic reticulum	2	1	0.0108268	1
GO:1905552	BP	positive regulation of protein localization to endoplasmic reticulum	2	1	0.0108268	1
GO:0005046	MF	KDEL sequence binding	3	1	0.0108284	1
GO:0019098	BP	reproductive behavior	30	2	0.0109375	1
GO:1905636	BP	positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding	3	1	0.0109386	1
GO:0035936	BP	testosterone secretion	2	1	0.0111017	1
GO:2000843	BP	regulation of testosterone secretion	2	1	0.0111017	1
GO:2000845	BP	positive regulation of testosterone secretion	2	1	0.0111017	1
GO:0072299	BP	negative regulation of metanephric glomerulus development	1	1	0.0111036	1
GO:0072302	BP	negative regulation of metanephric glomerular mesangial cell proliferation	1	1	0.0111036	1
GO:0071284	BP	cellular response to lead ion	3	1	0.0111855	1
GO:0035023	BP	regulation of Rho protein signal transduction	79	3	0.0112261	1
GO:1903895	BP	negative regulation of IRE1-mediated unfolded protein response	5	1	0.0114765	1
GO:0004382	MF	guanosine-diphosphatase activity	2	1	0.0115044	1
GO:1902626	BP	assembly of large subunit precursor of preribosome	3	1	0.0115739	1
GO:0047191	MF	1-alkylglycerophosphocholine O-acyltransferase activity	1	1	0.0117615	1
GO:2001246	BP	negative regulation of phosphatidylcholine biosynthetic process	1	1	0.0117615	1
GO:0003908	MF	methylated-DNA-[protein]-cysteine S-methyltransferase activity	1	1	0.0117914	1
GO:0043001	BP	Golgi to plasma membrane protein transport	39	2	0.0120581	1
GO:0050666	BP	regulation of homocysteine metabolic process	2	1	0.0125404	1
GO:0007612	BP	learning	140	4	0.0126947	1
GO:0014070	BP	response to organic cyclic compound	885	10	0.0129020	1
GO:0032870	BP	cellular response to hormone stimulus	602	8	0.0133645	1
GO:0045907	BP	positive regulation of vasoconstriction	33	2	0.0134807	1
GO:0006304	BP	DNA modification	116	3	0.0138524	1
GO:1990564	BP	protein polyufmylation	5	1	0.0138602	1
GO:1990592	BP	protein K69-linked ufmylation	5	1	0.0138602	1
GO:0090360	BP	platelet-derived growth factor production	3	1	0.0139227	1
GO:0090361	BP	regulation of platelet-derived growth factor production	3	1	0.0139227	1
GO:0008585	BP	female gonad development	96	3	0.0140875	1
GO:0047159	MF	1-alkenylglycerophosphocholine O-acyltransferase activity	2	1	0.0144966	1
GO:0050200	MF	plasmalogen synthase activity	2	1	0.0144966	1
GO:0044706	BP	multi-multicellular organism process	204	4	0.0146238	1
GO:0001544	BP	initiation of primordial ovarian follicle growth	2	1	0.0151198	1
GO:0005150	MF	interleukin-1, type I receptor binding	2	1	0.0152167	1
GO:0072301	BP	regulation of metanephric glomerular mesangial cell proliferation	2	1	0.0155594	1
GO:1900169	BP	regulation of glucocorticoid mediated signaling pathway	2	1	0.0155805	1
GO:0047192	MF	1-alkylglycerophosphocholine O-acetyltransferase activity	3	1	0.0156545	1
GO:0071963	BP	establishment or maintenance of cell polarity regulating cell shape	2	1	0.0158844	1
GO:0045764	BP	positive regulation of cellular amino acid metabolic process	3	1	0.0162795	1
GO:0016206	MF	catechol O-methyltransferase activity	2	1	0.0163029	1
GO:0102084	MF	L-dopa O-methyltransferase activity	2	1	0.0163029	1
GO:0102938	MF	orcinol O-methyltransferase activity	2	1	0.0163029	1
GO:0046545	BP	development of primary female sexual characteristics	100	3	0.0163060	1
GO:0034059	BP	response to anoxia	3	1	0.0164205	1

Including buccal

metal_all_cell_DVP = read.table('/Users/annebozack/Documents/arsenic_meta/generic-metal/all_cell_common_DVP_1204201.tbl', sep = "\t")

metal_all_cell_DVP = metalProcess(metal_all_cell_DVP)

write.csv(metal_all_cell_DVP, '/Users/annebozack/Documents/arsenic_meta/generic-metal/DVP_all_cell_common_120420.csv')


# Significant probes

# Nominal P-value
table(metal_all_cell_DVP$P.value < 0.05)
#  FALSE   TRUE 
# 348952  28399 

# FDR
table(metal_all_cell_DVP$P.FDR < 0.05)
# FALSE   TRUE 
# 377332     19 

table(metal_all_cell_DVP$P.FDR < 0.1)
 # FALSE   TRUE 
# 377245    106 

# Bonferroni
table(metal_all_cell_DVP$P.Bonf < 0.05)
# FALSE     TRUE
# 377346      5 


# GO analysis, FDR < 0.1 probes

go_metal_all_cell_DVP = gometh(sig.cpg = metal_all_cell_DVP$Name[metal_all_cell_DVP$P.FDR < 0.1], all.cpg = metal_all_cell_DVP$Name, array.type = '450K', anno = annAll2)
go_metal_all_cell_DVP = go_metal_all_cell_DVP[order(go_metal_all_cell_DVP$P.DE),]

table(go_metal_all_cell_DVP$P.DE<0.05)
# FALSE  TRUE 
# 22314   269  

table(go_metal_all_cell_DVP$FDR<0.05)
# FALSE 
# 22583 

write.csv(go_metal_all_cell_DVP[go_metal_all_cell_DVP$P.DE<0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/GO_DVP_all_cell_common_120420.csv')


# KEGG analysis, FDR < 0.1 probes

kegg_metal_all_cell_DVP = gometh(sig.cpg = metal_all_cell_DVP$Name[metal_all_cell_DVP$P.FDR < 0.1], all.cpg = metal_all_cell_DVP$Name, array.type = '450K', collection = 'KEGG', sig.genes = T, anno = annAll2)
kegg_metal_all_cell_DVP = kegg_metal_all_cell_DVP[order(kegg_metal_all_cell_DVP$P.DE),]

table(kegg_metal_all_cell_DVP$P.DE<0.05)
# FALSE  TRUE 
#  336     4

table(kegg_metal_all_cell_DVP$FDR<0.05)
# FALSE 
# 340 

write.csv(kegg_metal_all_cell_DVP[kegg_metal_all_cell_DVP$P.DE < 0.05,], '/Users/annebozack/Documents/arsenic_meta/generic-metal/KEGG_DVP_all_cell_common_120420.csv')




# Plotting

gg_qqplot(metal_all_cell_DVP$P.value)
quartz.save('qq_metal_all_cell_DVP_120420.png', type = "png", dpi = 300)

manhattan_meta(metal_all_cell_DVP, FDR=T)
quartz.save('manhattan_metal_all_cell_DVP_120420.png', type = "png", dpi = 300)

volcano_meta(metal_all_cell_DVP, FDR = TRUE)
quartz.save('volcano_metal_all_cell_DVP_120420.png', type = "png", dpi = 300)

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/qq_metal_all_cell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/manhattan_metal_all_cell_DVP_120420.png")

knitr::include_graphics("/Users/annebozack/Documents/arsenic_meta/generic-metal/volcano_metal_all_cell_DVP_120420.png")

Top 100 probes

X	Name	Effect	StdErr	P.value	Direction	P.FDR	P.Bonf	chr	pos	UCSC_RefGene_Name	UCSC_RefGene_Group
321132	cg23281729	0.9945	0.1300	0.00e+00	-+++	0.0000000	0.0000000	chr18	78005477	PARD6G	TSS200
374163	cg27425262	0.8952	0.1237	0.00e+00	++++	0.0000001	0.0000002	chr2	113953981	PSD4;LOC440839	Body;Body
50934	cg03205258	0.6446	0.1117	0.00e+00	++++	0.0010001	0.0030003	chr22	19929274	TXNRD2;COMT;COMT	1stExon;1stExon;5’UTR
163279	cg11032634	0.6967	0.1285	1.00e-07	++++	0.0056225	0.0224901	chr22	19929254	TXNRD2;COMT	1stExon;TSS200
64158	cg04080724	0.1394	0.0263	1.00e-07	++++	0.0085810	0.0429048	chr4	140202327	C4orf49	TSS1500
360213	cg26384602	-0.1222	0.0234	2.00e-07	—-	0.0102424	0.0705646	chr19	41798386	HNRNPUL1;HNRNPUL1	Body;Body
167567	cg11361658	0.1562	0.0300	2.00e-07	++++	0.0102424	0.0716967	chr5	128452311
145256	cg09692492	-0.2979	0.0576	2.00e-07	—-	0.0109290	0.0874322	chr22	23744717	ZDHHC8P	Body
314099	cg22749736	0.1176	0.0232	4.00e-07	++++	0.0175929	0.1583365	chr11	1306759	TOLLIP	Body
304645	cg21921619	-0.1465	0.0292	5.00e-07	-+–	0.0206675	0.2066751	chr10	116852791	ATRNL1	TSS1500
120767	cg07935287	-0.1330	0.0269	8.00e-07	—-	0.0257416	0.2984469	chr18	54318347	WDR7;WDR7	TSS1500;TSS1500
80568	cg05169951	0.2169	0.0440	8.00e-07	++++	0.0257416	0.3088995	chr16	3017955	KREMEN2;PAQR4;KREMEN2	Body;TSS1500;Body
295936	cg21185289	0.3705	0.0758	1.00e-06	++++	0.0293463	0.3815019	chr2	74743437	TLX2	3’UTR
309909	cg22387890	0.4772	0.0980	1.10e-06	++++	0.0302689	0.4237652	chr7	6145595	USP42	5’UTR
190387	cg13171197	0.1174	0.0244	1.50e-06	+-++	0.0366266	0.5524419	chr7	90916020
339841	cg24754507	-0.1026	0.0214	1.60e-06	—-	0.0366266	0.5860261	chr6	28481862	GPX6	Body
5963	cg00355447	0.1410	0.0295	1.80e-06	++++	0.0392864	0.6792318	chr6	30292220	HCG18;HCG18	Body;Body
237588	cg16511076	0.1215	0.0255	1.90e-06	+++-	0.0392864	0.7071558	chr4	48887480	OCIAD2;OCIAD2	3’UTR;3’UTR
76120	cg04873963	-0.1029	0.0218	2.50e-06	—-	0.0487577	0.9263967	chr16	2518322
124685	cg08207566	0.1154	0.0246	2.80e-06	+++-	0.0533763	1.0000000	chr4	174086461
102811	cg06740986	0.0989	0.0213	3.30e-06	++++	0.0588488	1.0000000	chr1	184838417	FAM129A	Body
167176	cg11332363	0.2113	0.0456	3.50e-06	++++	0.0598616	1.0000000	chr19	54023999	ZNF331	TSS200
302848	cg21774561	0.1147	0.0248	3.70e-06	++++	0.0604862	1.0000000	chr17	80209247	CSNK1D;CSNK1D	Body;Body
219690	cg15104380	-0.0861	0.0186	3.80e-06	+—	0.0604862	1.0000000	chr10	99285205	UBTD1	Body
303849	cg21857098	0.1019	0.0222	4.60e-06	++++	0.0647340	1.0000000	chr15	25638137	UBE3A;UBE3A;UBE3A	Body;Body;Body
293675	cg21004290	0.1266	0.0277	4.80e-06	++++	0.0647340	1.0000000	chr8	131250320	ASAP1	Body
193559	cg13411311	-0.1008	0.0220	4.80e-06	—-	0.0647340	1.0000000	chr2	241095989
161566	cg10898607	-0.1144	0.0250	4.80e-06	—-	0.0647340	1.0000000	chr3	101405733	RPL24	TSS200
129911	cg08575722	-0.1427	0.0313	5.10e-06	—-	0.0647340	1.0000000	chr11	32421845	WT1;WT1;WT1;WT1	Body;Body;Body;Body
189046	cg13054212	0.0959	0.0211	5.30e-06	++++	0.0647340	1.0000000	chr4	186356202	C4orf47	Body
214646	cg14718822	-0.1498	0.0329	5.30e-06	-+–	0.0647340	1.0000000	chr6	84234250	PRSS35;PRSS35	Body;Body
28677	cg01783101	0.2343	0.0517	5.80e-06	++++	0.0653810	1.0000000	chr7	118498931
334867	cg24376022	0.1055	0.0233	6.10e-06	++++	0.0653810	1.0000000	chr2	3215598	TSSC1	Body
11047	cg00657529	0.0940	0.0208	6.30e-06	++++	0.0653810	1.0000000	chr6	31698687	CLIC1;DDAH2	Body;TSS1500
191734	cg13281248	0.1068	0.0237	6.50e-06	++++	0.0653810	1.0000000	chr4	1244360	C4orf42;CTBP1;CTBP1;C4orf42	5’UTR;TSS1500;TSS1500;1stExon
179110	cg12235073	0.1203	0.0267	6.50e-06	++-+	0.0653810	1.0000000	chr10	6270423	PFKFB3;PFKFB3	Body;Body
243979	cg16991858	0.0921	0.0204	6.60e-06	++++	0.0653810	1.0000000	chr1	244612113	ADSS	Body
337569	cg24587312	-0.0682	0.0151	6.60e-06	++–	0.0653810	1.0000000	chr15	39766341
282709	cg20066496	-0.1849	0.0411	6.80e-06	+—	0.0654478	1.0000000	chr15	43213993	TTBK2	TSS1500
271236	cg19170881	-0.1914	0.0427	7.30e-06	—-	0.0654478	1.0000000	chr7	101129980	EMID2	Body
150964	cg10117884	0.1224	0.0273	7.40e-06	++++	0.0654478	1.0000000	chr1	166955898
162593	cg10980774	0.1646	0.0368	7.50e-06	++++	0.0654478	1.0000000	chr11	112832547	NCAM1;NCAM1;NCAM1	Body;Body;Body
119872	cg07875335	0.2405	0.0537	7.60e-06	++++	0.0654478	1.0000000	chr2	48844728	GTF2A1L;GTF2A1L;STON1-GTF2A1L	TSS1500;TSS1500;Body
126025	cg08293531	-0.0993	0.0222	7.80e-06	—-	0.0654478	1.0000000	chr15	101601180	LRRK1	Body
140791	cg09366379	-0.2971	0.0666	8.20e-06	—-	0.0654478	1.0000000	chr16	87905824
116190	cg07611790	0.0956	0.0215	8.40e-06	+++-	0.0654478	1.0000000	chr19	49240823	RASIP1	Body
292637	cg20923605	0.3039	0.0682	8.40e-06	++++	0.0654478	1.0000000	chr13	112978683
188976	cg13049359	0.1933	0.0434	8.50e-06	+-++	0.0654478	1.0000000	chr4	188891490
159378	cg10729167	0.1545	0.0347	8.60e-06	++++	0.0654478	1.0000000	chr10	111220101
23625	cg01445793	0.1912	0.0430	8.70e-06	++++	0.0654478	1.0000000	chr17	3771578	CAMKK1;CAMKK1;CAMKK1	Body;Body;Body
265593	cg18703721	0.1163	0.0262	9.40e-06	++++	0.0660776	1.0000000	chr10	75282672	USP54	Body
202666	cg13972353	0.1266	0.0286	9.50e-06	+++-	0.0660776	1.0000000	chr9	139354348	SEC16A	Body
178342	cg12175949	0.3017	0.0682	9.60e-06	++++	0.0660776	1.0000000	chr22	19929286	TXNRD2;COMT;COMT	1stExon;1stExon;5’UTR
148318	cg09920145	-0.0958	0.0216	9.60e-06	—-	0.0660776	1.0000000	chr3	69100714	TMF1	Body
125889	cg08285768	0.1000	0.0226	9.60e-06	+++-	0.0660776	1.0000000	chr15	86038622	AKAP13;AKAP13	Body;Body
144882	cg09664373	0.1149	0.0260	1.01e-05	++++	0.0661963	1.0000000	chr16	968219	LMF1	Body
232066	cg16101346	0.1496	0.0339	1.03e-05	-+++	0.0661963	1.0000000	chr1	186650479	PTGS2	TSS1500
300598	cg21575923	-0.1390	0.0315	1.03e-05	—-	0.0661963	1.0000000	chr6	41139345
110491	cg07219314	-0.1723	0.0391	1.03e-05	—-	0.0661963	1.0000000	chr22	23744725	ZDHHC8P	Body
18378	cg01105932	0.1049	0.0239	1.17e-05	++++	0.0723453	1.0000000	chr5	158635248	RNF145	TSS1500
156000	cg10485752	0.1432	0.0327	1.20e-05	++++	0.0723453	1.0000000	chr1	26021655	MAN1C1	Body
11224	cg00668103	0.1210	0.0277	1.22e-05	+++-	0.0723453	1.0000000	chr7	100084730	C7orf51	Body
37478	cg02339198	0.1076	0.0246	1.22e-05	++++	0.0723453	1.0000000	chr19	52693970	PPP2R1A	Body
33262	cg02067580	-0.0638	0.0146	1.23e-05	+—	0.0723453	1.0000000	chr1	153606662	C1orf77;S100A13;C1orf77	5’UTR;TSS200;1stExon
280471	cg19891452	0.2885	0.0660	1.25e-05	++++	0.0725094	1.0000000	chr13	112978703
235393	cg16353272	0.0961	0.0221	1.35e-05	++++	0.0736778	1.0000000	chr16	2124240	TSC2;TSC2;TSC2	Body;Body;Body
114654	cg07510163	0.1519	0.0349	1.36e-05	++++	0.0736778	1.0000000	chr2	44547313	PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;SLC3A1;PREPL	3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;3’UTR;Body;3’UTR
32578	cg02026246	0.1296	0.0299	1.44e-05	++++	0.0736778	1.0000000	chr11	22687589	GAS2	TSS1500
370643	cg27155653	-0.1019	0.0235	1.44e-05	—-	0.0736778	1.0000000	chr1	183604774	ARPC5;RGL1	1stExon;TSS1500
64658	cg04111999	0.1023	0.0236	1.46e-05	++++	0.0736778	1.0000000	chr10	22615540	BMI1	Body
131033	cg08654960	-0.1495	0.0345	1.46e-05	—-	0.0736778	1.0000000	chr16	85319859
109701	cg07168204	0.1217	0.0281	1.46e-05	+++-	0.0736778	1.0000000	chr5	149864599
280816	cg19916330	0.1027	0.0237	1.47e-05	++++	0.0736778	1.0000000	chr14	68038877	PLEKHH1	Body
259615	cg18228116	0.3476	0.0803	1.49e-05	-+++	0.0736778	1.0000000	chr10	133995345	JAKMIP3	3’UTR
98154	cg06421138	0.1083	0.0250	1.51e-05	++++	0.0736778	1.0000000	chr6	111750934	REV3L	Body
238518	cg16573251	0.0700	0.0162	1.53e-05	++++	0.0736778	1.0000000	chr12	123381231	VPS37B	TSS1500
339775	cg24748746	-0.2174	0.0503	1.53e-05	—-	0.0736778	1.0000000	chr7	155738916
291461	cg20805880	0.1014	0.0234	1.53e-05	++++	0.0736778	1.0000000	chr15	73367293	NEO1	Body
121453	cg07984508	0.0906	0.0210	1.56e-05	+++-	0.0736778	1.0000000	chr15	77426719	SGK269	Body
112621	cg07367760	0.1087	0.0252	1.56e-05	++++	0.0736778	1.0000000	chr16	2911707
147224	cg09845489	0.2497	0.0579	1.63e-05	++++	0.0749701	1.0000000	chr7	157667853	PTPRN2;PTPRN2;PTPRN2	Body;Body;Body
146726	cg09809672	-0.1376	0.0319	1.64e-05	—-	0.0749701	1.0000000	chr1	236557682	EDARADD;EDARADD;EDARADD	TSS1500;5’UTR;1stExon
316511	cg22938135	0.0935	0.0217	1.65e-05	+++-	0.0749701	1.0000000	chr5	175841493	CLTB;CLTB	Body;Body
100415	cg06581201	0.1743	0.0405	1.67e-05	++++	0.0749760	1.0000000	chr6	168534038
93087	cg06039392	0.1302	0.0303	1.70e-05	++++	0.0754702	1.0000000	chr4	187476953	MTNR1A	TSS1500
343712	cg25052374	0.0771	0.0180	1.78e-05	++++	0.0777924	1.0000000	chr17	76991253	CANT1;CANT1;CANT1	Body;Body;Body
307323	cg22159421	-0.3143	0.0733	1.82e-05	—-	0.0777924	1.0000000	chr11	34460182	CAT	TSS1500
190817	cg13208054	0.0753	0.0176	1.83e-05	++++	0.0777924	1.0000000	chr17	25936354	KSR1	Body
58507	cg03700279	0.1001	0.0234	1.86e-05	+++-	0.0777924	1.0000000	chr2	44576358	PREPL;PREPL;PREPL;PREPL;PREPL;PREPL;PREPL	Body;Body;5’UTR;5’UTR;Body;Body;Body
156274	cg10502904	0.1460	0.0341	1.87e-05	++++	0.0777924	1.0000000	chr10	131565289	MGMT	3’UTR
301085	cg21613693	-0.1303	0.0304	1.88e-05	—-	0.0777924	1.0000000	chr17	73501181	CASKIN2;CASKIN2	Body;Body
227727	cg15754901	0.1049	0.0246	1.99e-05	+-++	0.0816637	1.0000000	chr17	5402972	LOC728392	3’UTR
336897	cg24531494	0.1549	0.0365	2.15e-05	++++	0.0871965	1.0000000	chr4	121993049	C4orf31	5’UTR
69534	cg04426031	0.1100	0.0260	2.27e-05	++++	0.0905245	1.0000000	chr7	1799192
114218	cg07479711	0.1114	0.0263	2.28e-05	++++	0.0905245	1.0000000	chr5	1524940	LPCAT1	TSS1500
248409	cg17332762	0.0966	0.0228	2.31e-05	+++-	0.0906822	1.0000000	chr3	106967639	LOC344595;LOC344595	Body;Body
35145	cg02192228	0.1758	0.0416	2.38e-05	++++	0.0921815	1.0000000	chr3	8809536	OXTR	Body
171628	cg11691429	0.1703	0.0403	2.39e-05	+++-	0.0921815	1.0000000	chr2	947634	SNTG2	Body
128672	cg08487455	0.1666	0.0395	2.46e-05	++++	0.0936517	1.0000000	chr16	76311050	CNTNAP4	TSS200
202290	cg13946520	0.2956	0.0701	2.48e-05	-+++	0.0936585	1.0000000	chr2	87017689	CD8A;CD8A;CD8A;CD8A	Body;Body;Body;Body

---

Top 100 GO terms

X	ONTOLOGY	TERM	N	DE	P.DE	FDR
GO:0016209	MF	antioxidant activity	83	4	0.0003353	1
GO:0098869	BP	cellular oxidant detoxification	97	4	0.0008096	1
GO:0004601	MF	peroxidase activity	49	3	0.0009488	1
GO:1990748	BP	cellular detoxification	107	4	0.0010205	1
GO:2000171	BP	negative regulation of dendrite development	25	3	0.0010763	1
GO:0016684	MF	oxidoreductase activity, acting on peroxide as acceptor	53	3	0.0012599	1
GO:0097237	BP	cellular response to toxic substance	114	4	0.0016410	1
GO:0098754	BP	detoxification	130	4	0.0016700	1
GO:0005794	CC	Golgi apparatus	1477	17	0.0030512	1
GO:0099631	CC	postsynaptic endocytic zone cytoplasmic component	2	1	0.0031425	1
GO:0005078	MF	MAP-kinase scaffold activity	11	2	0.0036667	1
GO:0030728	BP	ovulation	20	2	0.0043379	1
GO:0051232	BP	meiotic spindle elongation	1	1	0.0047115	1
GO:0004990	MF	oxytocin receptor activity	1	1	0.0049495	1
GO:0050774	BP	negative regulation of dendrite morphogenesis	14	2	0.0052437	1
GO:0032225	BP	regulation of synaptic transmission, dopaminergic	16	2	0.0053970	1
GO:0010335	BP	response to non-ionic osmotic stress	1	1	0.0059936	1
GO:0071471	BP	cellular response to non-ionic osmotic stress	1	1	0.0059936	1
GO:0061000	BP	negative regulation of dendritic spine development	11	2	0.0060264	1
GO:0010288	BP	response to lead ion	22	2	0.0067367	1
GO:0004666	MF	prostaglandin-endoperoxide synthase activity	2	1	0.0073230	1
GO:0090362	BP	positive regulation of platelet-derived growth factor production	2	1	0.0075212	1
GO:0050886	BP	endocrine process	78	3	0.0076888	1
GO:0051704	BP	multi-organism process	1013	11	0.0080764	1
GO:0097711	BP	ciliary basal body-plasma membrane docking	91	3	0.0103511	1
GO:0001990	BP	regulation of systemic arterial blood pressure by hormone	35	2	0.0105805	1
GO:0001992	BP	regulation of systemic arterial blood pressure by vasopressin	4	1	0.0106572	1
GO:0035037	BP	sperm entry	1	1	0.0108844	1
GO:0061795	BP	Golgi lumen acidification	1	1	0.0108844	1
GO:1905526	BP	regulation of Golgi lumen acidification	1	1	0.0108844	1
GO:1905528	BP	positive regulation of Golgi lumen acidification	1	1	0.0108844	1
GO:1903537	BP	meiotic cell cycle process involved in oocyte maturation	2	1	0.0112336	1
GO:1903538	BP	regulation of meiotic cell cycle process involved in oocyte maturation	2	1	0.0112336	1
GO:0048545	BP	response to steroid hormone	329	6	0.0116089	1
GO:0019953	BP	sexual reproduction	791	9	0.0117434	1
GO:0050321	MF	tau-protein kinase activity	22	2	0.0117656	1
GO:0031337	BP	positive regulation of sulfur amino acid metabolic process	1	1	0.0119192	1
GO:0050668	BP	positive regulation of homocysteine metabolic process	1	1	0.0119192	1
GO:0071284	BP	cellular response to lead ion	3	1	0.0120588	1
GO:0045987	BP	positive regulation of smooth muscle contraction	31	2	0.0121754	1
GO:1902626	BP	assembly of large subunit precursor of preribosome	3	1	0.0122891	1
GO:0048609	BP	multicellular organismal reproductive process	769	9	0.0124007	1
GO:0035936	BP	testosterone secretion	2	1	0.0124744	1
GO:2000843	BP	regulation of testosterone secretion	2	1	0.0124744	1
GO:2000845	BP	positive regulation of testosterone secretion	2	1	0.0124744	1
GO:0004382	MF	guanosine-diphosphatase activity	2	1	0.0132654	1
GO:0032504	BP	multicellular organism reproduction	789	9	0.0133388	1
GO:0044703	BP	multi-organism reproductive process	943	10	0.0136047	1
GO:0072299	BP	negative regulation of metanephric glomerulus development	1	1	0.0140367	1
GO:0072302	BP	negative regulation of metanephric glomerular mesangial cell proliferation	1	1	0.0140367	1
GO:0019098	BP	reproductive behavior	30	2	0.0140944	1
GO:0050666	BP	regulation of homocysteine metabolic process	2	1	0.0143875	1
GO:0004046	MF	aminoacylase activity	5	1	0.0145101	1
GO:1904527	BP	negative regulation of microtubule binding	2	1	0.0147022	1
GO:0043001	BP	Golgi to plasma membrane protein transport	39	2	0.0147435	1
GO:0090360	BP	platelet-derived growth factor production	3	1	0.0148222	1
GO:0090361	BP	regulation of platelet-derived growth factor production	3	1	0.0148222	1
GO:0008446	MF	GDP-mannose 4,6-dehydratase activity	1	1	0.0148750	1
GO:0047191	MF	1-alkylglycerophosphocholine O-acyltransferase activity	1	1	0.0152431	1
GO:2001246	BP	negative regulation of phosphatidylcholine biosynthetic process	1	1	0.0152431	1
GO:0003908	MF	methylated-DNA-[protein]-cysteine S-methyltransferase activity	1	1	0.0152953	1
GO:0001963	BP	synaptic transmission, dopaminergic	27	2	0.0157612	1
GO:0010193	BP	response to ozone	4	1	0.0157812	1
GO:0004019	MF	adenylosuccinate synthase activity	2	1	0.0158240	1
GO:1902816	BP	regulation of protein localization to microtubule	5	1	0.0166441	1
GO:1902817	BP	negative regulation of protein localization to microtubule	5	1	0.0166441	1
GO:0045907	BP	positive regulation of vasoconstriction	33	2	0.0167987	1
GO:0033596	CC	TSC1-TSC2 complex	2	1	0.0169103	1
GO:0051754	BP	meiotic sister chromatid cohesion, centromeric	4	1	0.0170654	1
GO:0001544	BP	initiation of primordial ovarian follicle growth	2	1	0.0173561	1
GO:0014065	BP	phosphatidylinositol 3-kinase signaling	152	4	0.0174938	1
GO:0047159	MF	1-alkenylglycerophosphocholine O-acyltransferase activity	2	1	0.0179564	1
GO:0050200	MF	plasmalogen synthase activity	2	1	0.0179564	1
GO:0021935	BP	cerebellar granule cell precursor tangential migration	2	1	0.0180708	1
GO:0008502	MF	melatonin receptor activity	3	1	0.0182369	1
GO:0033365	BP	protein localization to organelle	927	10	0.0183281	1
GO:0034059	BP	response to anoxia	3	1	0.0183810	1
GO:0045764	BP	positive regulation of cellular amino acid metabolic process	3	1	0.0185377	1
GO:0072301	BP	regulation of metanephric glomerular mesangial cell proliferation	2	1	0.0188547	1
GO:0016206	MF	catechol O-methyltransferase activity	2	1	0.0188997	1
GO:0102084	MF	L-dopa O-methyltransferase activity	2	1	0.0188997	1
GO:0102938	MF	orcinol O-methyltransferase activity	2	1	0.0188997	1
GO:1900169	BP	regulation of glucocorticoid mediated signaling pathway	2	1	0.0189176	1
GO:0010701	BP	positive regulation of norepinephrine secretion	4	1	0.0190142	1
GO:0042713	BP	sperm ejaculation	5	1	0.0191454	1
GO:0047192	MF	1-alkylglycerophosphocholine O-acetyltransferase activity	3	1	0.0191847	1
GO:0005150	MF	interleukin-1, type I receptor binding	2	1	0.0192514	1
GO:0023024	MF	MHC class I protein complex binding	5	1	0.0193178	1
GO:0032227	BP	negative regulation of synaptic transmission, dopaminergic	3	1	0.0193314	1
GO:0016036	BP	cellular response to phosphate starvation	2	1	0.0193647	1
GO:0043262	MF	adenosine-diphosphatase activity	2	1	0.0194854	1
GO:0031335	BP	regulation of sulfur amino acid metabolic process	3	1	0.0195627	1
GO:0042351	BP	‘de novo’ GDP-L-fucose biosynthetic process	2	1	0.0195690	1
GO:0008585	BP	female gonad development	96	3	0.0201038	1
GO:0031394	BP	positive regulation of prostaglandin biosynthetic process	7	1	0.0202188	1
GO:0060359	BP	response to ammonium ion	4	1	0.0202812	1
GO:1905424	BP	regulation of Wnt-mediated midbrain dopaminergic neuron differentiation	2	1	0.0203327	1
GO:1905426	BP	positive regulation of Wnt-mediated midbrain dopaminergic neuron differentiation	2	1	0.0203327	1
GO:0044208	BP	‘de novo’ AMP biosynthetic process	3	1	0.0203449	1
GO:0003044	BP	regulation of systemic arterial blood pressure mediated by a chemical signal	45	2	0.0203784	1